Biology Exam 4

How does a bacterium divide though binary fission and how chloroplast and mitochondria replicate?

1. cell grows in volume and length

2. circular chromosomes replicate and separate

3. cell elongates and forms cell wall in middle

4. plasma membrane forms in each cell

5. cell divides into 2 identical cells

image on pg 1

Learn the terms chromosomes, chromatid and chromatin. What stages of cell cycle they are visible?

chromosome - ??? - prophase

chromatid - 1 of the 2 replicated chromosomes - anaphase

chromatin - goes through condensation to form chromosome - ????

Know the sequence of stages of cell cycle, including the 3 phases of interphase and mitotic phase.

interphase -

G1 → S → G2

mitotic -

prophase → prometaphase → metaphase → anaphase → telophase → cytokinesis

Learn how each phase of "interphase" is defined, the changes that take place at each stage.

G1 - cell grows and metabolic activity - checkpoint to decide if they want to divide (enter S-phase) or not (G0 phase)

S - DNA/chromosome replicates

G2 - growth and final preparation (all organelles and membranes are duplicated)

G0 phase

not actively preparing to divide

-stay temporarily - until environmental conditions improve or external signal triggers

-stay permanently when they never or rarely divide

Prophase

-nucleus is intact

-nucleolus disappears

-chromatin gets denser and forms chromosomes

-2 pairs of centrioles move to opposite poles

Prometaphase

-nuclear envelope breaks and disappears

-microtubules of spindle fibers are connected to chromosome at kinetochore (form sister chromatids)

-chromosomes become more condensed

-polar microtubules elongate

Metaphase

-sister chromatids of replicated chromosomes are aligned in middle of cell and maximally condensed

Anaphase

-centromere of each chromosome divides

-sister chromatids split to form 2 single stranded chromosomes

Cytokinesis

-animals: cleavage furrow (cytoplasm furrows inward)

-plants: cell plate forms to divide 2 daughter cells

-cells enter interphase again to grow and develop or divide again

Telophase

-2 nuclei form to envelope 2 new groups of daughter chromosomes

-nucleoli reappear inside each nucleus

-chromosomes loosen to become chromatin again

How does cytokinesis take place in animal and plant cells that results in two cells?

animals: cleavage furrow - cytoplasm furrows inward → divides into 2 cells

plants: cell plate forms to divide 2 daughter cells

What are the significances of checkpoints and internal & external conditions that are monitored by cell to determine whether to divide and whether to progress from one stage to another?

???

How do cyclin and CDK serve as major components controlling checkpoints in cell cycle and the MPF activity peaks during M phase and S phase?

cyclin binds to CDK → forms MPF (S-MPF initiates S-phase) (M-MPHF initiates M-phase)

Learn the changes in ploidy level (chromosome number) and the DNA amount in meiosis (reduction division).

chromosome #:

-I 1: 1x

-P 1: 1x

-M 1: 1x

-A 1: .5x

-T 1: .5x

-I 2: .5

-P 2: .5x

-M 2: .5x

-A 2: .5x

-T 2: .5x

DNA:

-I 1: 2x

-P 1: 2x

-M 1: 2x

-A 1: 1x

-T 1: 1x

-I 2: 1x

-P 2: 2x

-M 2: 2x

-A 2: 1x

-T 2: .5x

Remember all the stages of meiosis I

Interphase I:

-chromosomes replicate into 2 sister chromatids

Prophase I:

-most important stage

-homologous chromosomes align themselves to form tetrads (2 X's)

-crossing over - overlapping of homologous chromosomes

-recombination - DNA exchange

-chiasmata - X-shaped regions crossing over

Metaphase I:

-tetrads align themselves in the middle along metaphase plate

-independent assortment of chromosome

Anaphase I:

-individual sister chromatids separate from each other (2 X's split up) and go to opposite poles (sister chromatids are still attached)

Telophase I:

-2 daughter cells are formed = "haploids"

-nuclear envelope can form and divides cell

Remember all the stages of meiosis II

Interphase II:

-no DNA replication happens

Prophase II:

-nucleus and nucleolus disappear and spindle fibers appear on both sides of centromere

-if chromosomes decondensed in telophase I → condense again

-if nuclear envelopes formed → chromosomes fragment into vesicles

Metaphase II:

-sister chromatids align on metaphase plate

-sister chromatids are maximally condensed

Anaphase II:

-centromeres of sister chromatids separate and individual chromosomes move towards opposite ends

Telophase II:

-nuclei forms around chromosomes

-cleavage furrow or cell plate separates new daughter cells

-4 cells formed = haploid

Know the three causes of genetic variation in sexual reproduction and what stages these occur in sexual reproduction.

crossing over - chromosomes exchange DNA - occurs in prophase I

independent assortment - tetrads randomly aligning themselves on metaphase plate - occurs in metaphase I

random fertilization - DNA egg and sperm randomly combine

Be able to recognize the various stages of mitosis and meiosis.

Understand the experiments that proved DNA as the genetic material.

"transforming principle":

-S-strain → caused disease

-R-strain → did not cause disease

-killed S-strain with heat → did not cause disease

-killed S-strain with heat + R-strain → caused disease

-concluded that the heat that killed S-strain transformed R-strain by transferring "genetic principle"

Avery, McLeod, McCarty:

-isolated DNA from S-strain → mixed with R-strain to transform into disease causing strain

-when DNA degraded → no longer able to transform bacteria → DNA was transforming principle

-RNase and Protease cause disease (R-strain became S-strain)

-DNase did not cause disease (no transformation)

Hershey and Chase:

-bacteriophage attaches to host bacterial cell and injects nucleic acids inside bacterial cell → DNA makes many copies → host cell bursts and release many bacteriophages

-in the end, bacteria contained most of DNA → DNA was genetic material injected into bacterial cells to program cells to make more viruses

Be able to predict the results, if the experimental conditions were changed.

What is the structure of DNA double helixes described by Watson and Crick? Pay attention to all the details and know how DNA stores information.

-2 strands are H-bonded together

-2 strands turn right to make right-handed helix

-hydrophilic sugar-phosphate is on outside of helix

-hydrophobic nitrogenous bases are inside

-A:T with 2 H-bonds

-C:G with 3 H-bonds

-DNA stores information in sequence of bases (4 bases with infinite possibilities of various sequence and lengths)

Understand the semiconservative mode of DNA replication and how it was proved. Be able to predict the outcome if the methods are changed.

semiconservative - new DNA is made up of one old strand as template and new strand based on complementary base pairings

proved:

-grew bacteria with 15N → added to 14N → let it replicate → separate each DNA replication based on DNA density (14N is lighter and is higher in the tube; 15N is heavier and is lower in tube)

-concluded that new DNA strand is combination of old and new DNA strands

Learn how the results proved the hypothesis and disproved the alternate hypothesis in all the experiments in this chapter.

??

Understand complementary base pairing of DNA and how it helps in the DNA replication process.

A=T (concentrations are equal)

G=C

???

What are the bonds and interactions that are essential in DNA double helix?

A:T - 2 H-bonds

C:G - 3 H-bonds

???

Know the terms ORI, replication bubble and replication fork.

ORI (origin of replication) - location on DNA molecule with specific sequence that is recognized by enzymes involved in DNA replication

replication bubble - ???

replication fork - ??

Remember all the enzymes and proteins involved in DNA replication, and their roles.

topoisomerase - relaxes supercoiling of DNA

helicase - unwinds double helix into 2 single stranded DNA

SSB - single-strand binding protein and stabilizes ssDNA

primase - synthesizes RNA primers

DNA polymerase I - removes RNA primers and inserts DNA in the gaps

DNA polymerase III - synthesizes DNA, proofreads, exonuclease activity and repair

DNA ligase - connects DNA fragments with phosphodiester linkage

DNA gyrase - introduces supercoiling in DNA

Know the sequence of events during DNA replication.

Initiation:

-topoisomerase relaxes supercoiling at origin of replication

-DNA helix is opened to make replication fork → single stranded DNA is stabilized by SSB proteins

-primase makes RNA primers for DNA polymerase to work → start new DNA synthesis

Elongation:

-DNA polymerase III binds to DNA template & RNA-primer region → add nucleotides that are complementary to template strand

-DNA is synthesized in small fragments → DNA polymerase II proofreads and removes errors

-DNA polymerase I removes RNA primers and completes DNA strand

???

Know the basic details about leading, lagging strand synthesis and Okazaki fragments.

leading strand - adds nucleotides from 5' to 3'

lagging strand - strand that contains okazaki fragments and is made slowly after leading strand

Okazaki fragment - small fragments added from 3' to 5'

Why does the DNA replicate from 5' to 3'?

because nucleotides can only be added at the 5' end

What are the three major types of DNA repair processes and the enzymes involved in each of them?

Mismatch repair - corrects errors made during DNA replication - DNA polymerase III removes wrong bases and remakes DNA to minimize errors

Excision repair - gets rid of damaged strand of DNA (by endonuclease) and makes new matching strand in its place (by DNA polymerase II and DNA ligase)

Telomere repair - extends 3' end of telomere region and allows RNA primer to bind to extended region to protect telomere from being degrade - done by telomerase

What are the structural components of a eukaryotic gene?(Promoter, enhancer, intron, exon etc.)

promoter - DNA sequence where transcription machinery binds and imitates transcription (controls accuracy and how often)

enhancer/suppressor - bound by transcription factors results in more/less active transcription

intron - does not code for protein

exon - expressed regions coding for protein

What are the enzymes, cis-acting elements, trans-acting/transcription factors and steps involved in transcription?

trans-acting factors:

-recognize specific DNA sequences (aka cis-acting elements)

-bind to enhancer/suppressor or promoter

cis-acting elements:

-what transcription bind to

-on enhancer/suppressor or and promoter regions

steps:

-RNA polymerase bind to promoter to begin transcription

What steps, modifications and proteins are involved in the RNA processing in eukaryotes?

capping - add G-cap to 5' end of mRNA

polyadenylation - add poly(A) tails to 3' end of mRNA

RNA splicing - remove introns and combine exons

Understand coding strand, template strand and direction of transcription.

coding strand - ??

template strand - ???

direction of transcription:

-coding: 5' - 3'

-template: 3' - 5'

-mRNA: 5' - 3'

-protein: 3' - 5'

Describe the terms and details of codons, anticodons, degeneracy, wobble, promoter and one gene-one polypeptide experiment.

codon - 3 mRNA base pairs

anticodon - 3 complementary tRNA base pairs to codon

degeneracy - multiple codons code for one amino acid

wobble - 3rd base of tRNA can be "inosine" and can code for A, U, or C

one gene-one polypeptide - 1 gene codes for 1 enzyme, and any mutation in that gene will result in enzyme with that mutation

What are the different types of mutations?

point - one base is replaced by another

-silent - doesn't change the amino acid

-missense - changes amino acid

-non-sense - changes to stop codon

insertion/deletion - one base is inserted or deleted → frameshift

inversion - flipping the order of genes

translocation - moving part of chromosome from one place to another or to a different chromosome

What happens (specifically) during RNA processing in eukaryotic cells?

G-cap adds to 5' end of mRNA

poly(A) tail adds to 3' end of mRNA

introns are removed and exons are combined

What are the 3 types of RNA and their functions?

mRNA - carries message from one gene to be translated into protein

rRNA - have small and large subunits to coordinate protein synthesis coupling mRNA and tRNA

tRNA - functions as adapter between mRNA and amino acids being added to build protein during protein synthesis (also translates RNA into proteins)

What are the proteins and steps involved in amino acid activation?

1. binds to correct amino acid and attaches AMP by hydrolyzing ATP (forms high-energy bond between amino acid and AMP)

2. enzyme recognizes tRNA by secondary structure and anticodon

3. transfers amino acid to correct tRNA and AMP is detached → releases aminoacyl tRNA

What are the proteins and steps involved in the whole protein synthesis process? Know the details in each step.

Initiation:

-small subunit recognizes ribosome binding site

-tRNA carrying specific codon binds to P-site

3 initiation factors and GTP binds to form initiation complex

-large subunit

Elongation:

-codon recognition: brings next anticodon to A-site

-peptide bond: 1st codon (meth) transfers from P-site tRNA to A-site and makes peptide bond between previous amino acid and incoming amino acid - empty tRNA in P-site moves to E-site and leaves ribosome

-translocation: tRNA moves through A, P, E site and more amino acids are added to A-site

Termination:

-release factor adds H2O to last amino acid and releases protein, ribosomal coat, tRNA and mRNA

-ribosomes make protein on other mRNA

Remember the examples of protein processing in eukaryotes.

-amino terminal cleaved to activate protein or remove target signal

-disulfide bonds formed between 2 cystines

-some amino acid side chains are chemically modified

-glycosylation of some residues on protein

Compare and contrast prokaryotes and eukaryotes in transcription and translation.

prokaryotes:

-transcription and translation happen simultaneously in cytoplasm

-polycistronic - one gene codes for many proteins

-does not go through processing before translation (no introns)

eukaryotes:

-transcription & RNA processing happens in nucleus

-translation happens in cytoplasm

-monocistronic - one gene codes for one protein

-goes through processing (capping, polyadenylation, RNA splicing)

What are the needs of prokaryotes in gene regulation?

???

Know the details of prokaryotic operons-structure, inducible and repressible.

operon - has coding sequences of genes in a unit, promoter and operator - multiple genes are organized into a single transcriptional unit under control of a single promoter

Compare and contrast inducible & repressible operons, and their regulation.

inducible - control catabolic pathways used to break down compounds (lac operon)

-mostly turned off, turned on when necessary

-lactose & glucose present: prefers glucose → removes repressor on operator of lac operon → lactose binds to repressor molecule (inactive repressor) → start transcription

-only lactose: increase of cAMP levels → cAMP binds to CAP → CAP binds to promoter → increase rate of transcription

-no lactose: no transcription

repressible - used for anabolic pathways to synthesize compounds (Trp)

-most turned on, turned off when needed

-Trp absent: repressor protein inactive → transcription

Trp abundant: bind to repressor molecule (active repressor) → no transcription (RNA or proteins)

How is the eukaryotic genome organized? Identify the components at different levels of organization.

genome size:

-chromosomal DNA is dispersed as chromatin

-double helix of DNA wraps around histone proteins to form nucleosomes (condense more to make chromatin)

-chromosomes are linear molecules (ends are called telomeres)

repetitive DNA:

-most DNA is made of DNA sequences that don't code for any RNA or protein

-DNA is made up of repetitive DNA with 5-10 bases repeated thousands of times

-repetitive DNA can be identified by reannealing denatured DNA

-useful in DNA replication b/c they fold into themselves to provide 3'-OH group for DNA synthesis

multiple gene families:

-result of gene duplication during crossing over

-pseudogenes: duplicated copies of genes that mutate and evolve independently and lose their regulator sequences and are not expressed

-can be located together on chromosome or spread out on different chromosomes

-can be detected by DNA-DNA techniques

-coordinated gene expression: regulated by common cis-acting elements recognized by trans-acting factors specific for that gene family

What are the needs of eukaryotes in gene regulation?

-multicellular and different types of tissues

-undergoes growth and development

-contains introns

-transcription and translation are separated in time and space

What are the four levels of gene regulation in eukaryotes? Know specific examples.

transcriptional (long-term):

-DNA methylation

-compaction of chromosome

-insertion/deletion

-antibody variation

-DNA rearrangement

-acetylation

transcriptional (short-term):

-helix-turn-helix protein

-zinc finger

-leucine zippers

post-transcriptional:

-alternate splicing

-mRNA stability

translational:

-mRNA storage

-hormonal regulation (prolactin)

-timing (egg fertilized by sperm)

-effect of cofactor on translation (heme in hemoglobin)

post-translational:

-zymogen activation

-selective targeting

-chemical modification (phosphorylation)

-glycosylation

What are the roles the cis-acting elements (regulatory sequences) and trans-acting factors (transcription factors) in regulating gene expression?

cis-acting elements - specific sequences on DNA that are recognized by transcription factors (affects amount, rate and accuracy of transcription)

-promoter - determines how often gene is transcribed (signals RNA polymerase when to begin)

-enhancer - more active transcription

-suppressor - less active transcription

transcription factors - proteins that bind to DNA and affect transcription

Know the terms such as tissue-specific gene expression, transposable elements, gene amplification and coordinated gene regulation.

tissue-specific gene expression - genes are expressed in tissue-specific manner to facilitate function of different cell or tissue types (ex: leaf tissues in plants make protein for photosynthesis and storage tissues in seed will make storage proteins)

transposable elements - mobile genetic elements that transpose from one part of chromosome to another part or different chromosome - recognize specific DNA sequence in target region → cut DNA and insert themselves using enzyme transposes

gene amplification - genes get duplicated several times to amplify their number for enough copies of mRNAs to be produced

coordinated gene regulation - expression of multigene family members regulated by common trans-acting factors specific for that gene family (ex: globin genes code for subunits of hemogloblin)

What is so special about recombinant DNA technology not possible by classical breeding?

-cross species barrier

-allows for creation of multiple copies of genes and insertion of foreign genes to give them new traits

Learn some examples of enzymes used in recombinant DNA work and their functions.

restriction endonuclease - recognize specific DNA sequence and cleave the DNA at that recognition site

DNA polymerase - used to make DNA in vitro - also for DNA synthesis, DNA sequencing, polymerase chain reactions

DNA ligase - catalyze covalent bonding of 3' and 5' ends of 2 DNA strands (connect 2 strands) → make recombinant DNA molecule

reverse transcriptase - uses RNA template to make complementary DNA

What are the uses of DNA gel electrophoresis, sequencing, PCR, microarray and other methods discussed in class?

gel electrophoresis - fractionate DNA or RNA fragments based on size

DNA sequencing - extends the new strand of DNA from primer in suitable buffer

PCR - amplify large amounts of DNA from small amounts of samples (can clone new genes for identifying suspect)

microarray analysis - determines which genes are expressed among a group of several thousand genes

What are some applications of recombinant DNA technology in plants, animals and humans?

plants:

-herbicide resistance

-insect resistance

-virus/disease resistance

-fungal resistance

-improved storage quality

-improved nutrition

animals:

-introduce genes at early embryonic stage

-increase milk or meat production

-vaccines, cures, treatments

-therapeutics

-GMO (zebrafish, glow fish, fast growing salmon)

-cloning of prized animals

humans:

-genetic diseases

-diagnostics of disease or infection

-recombinant vaccines, diagnostics, treatment and cures

-gene therapy to fix genetic errors

-DNA detection (paternity testing, forensics, diagnostics at birth)

-identification of new virus

-produce proteins

Understand the safety and ethical concerns of recombinant DNA technology.

safety:

-avoid contamination, infection and mistakes that have potential to replicate quickly

-chemicals can interfere with DNA and cause mutations and pathogenic viruses

-FDA regulates recombinant products exposed to public

ethical concerns:

-question if it's ethical to do research

-implications: use of such information

Know the practical uses of various techniques in a given situation.

Be able to predict or interpret experimental results in recombinant DNA.