Study Guided Questions Exam #3

Describe the process of TRANSCRIPTION What are the steps of each? What is produced? How does splicing occur? What components are involved?

*Initiation* - Sigma recognizes promoter (-35 and -10 boxes of the promoter) - RNA polymerase - NTPs (ribonucleotides to produce mRNA) *Elongation* - Synthesizing RNA by complementary base pairing *Termination* - Signal to stop (hairpin structure in Bacteria; poly A signal in Eukaryotes) - Separates RNA transcript → Post-transcriptional Modification (Eukaryotes) Splicing (taking out introns, leave exons) 5' Cap and Poly A Tail (protection from degradation)

Describe the process of TRANSLATION What are the steps of each? What is produced? What components are involved?

*Initiation* - mRNA binds to the small subunit of the ribosome - Charged tRNA binds to start codon (AUG methionine) - Large attaches to small subunits *Elongation* - Arrival of the aminoacyl tRNA in the A site - P → Peptide chain Peptide bond formation - Charged tRNA brings in an amino acid to the A Spot - Peptide Bond - Translocation *Termination* - Stop codon for protein to be released - Uncharged protein - Hydrolyzes bond between chain and tRNA (PRF - protein release factor) → *Post-Translational Modification* (Eukaryotes) (Golgi Apparatus) - Glycosylation - Phosphorylation (activates or inactivates) - Protein Folding - Add sugars, lipids, or phosphate (kinase adds/activates; phosphatase remove)

What's the difference between prokaryotic and eukaryotic translation?

*Prokaryotic* circular and have ONE replication bubble Bacteria have concurrent transcription and translation No time to modify and fix *Eukaryotic* linear with multiple replication forks and bubbles Transcription and translation is separated Allows for modification

DNA replication: How does the leading strand replication differ from the lagging strand replication?

- Leading Strand: only has a beginner primer and DNA is made in the direction the template is unwound, so it makes DNA as a long continuous piece. - Lagging strand, has many RNA primers and the DNA is made in the opposite direction so it is made in Okazaki fragments, which are short pieces of DNA. Enzyme: DNA Polymerase III. (adds dNTPs to the RNA primers)

Describe the importance of checkpoints

- allows a cell to "decide"whether to proceed with division - If regulatory molecules are defective, the checkpoint may fail → tumor

Steps in DNA replication

1. DNA is unwound at origins of replication. Enzymes used; Helicase (unwinds DNA) & Topoisomerase (releases pressure in the kinks, unwinding the kinks) - Single stranded binding proteins (SSBP) bind to DNA and keep it single stranded (unwound) until it can be replicated Enzyme used: SSBP (bind to the DNA and hold it in unwound form). 2. RNA primer (a short piece of RNA that acts as a "starter" for DNA synthesis. Enzyme: Primase (makes the RNA primer) 3. DNA is synthesized in the 5' to 3' direction. - Leading Strand: only has a beginner primer and DNA is made in the direction the template is unwound, so it makes DNA as a long continuous piece. - Lagging strand, has many RNA primers and the DNA is made in the opposite direction so it is made in Okazaki fragments, which are short pieces of DNA. Enzyme: DNA Polymerase III. (adds dNTPs to the RNA primers) - Mismatched bases are removed by proofreading by DNA polymerase III, goes from 3' -> 5'. 4. Primers are removed and the gap is filled with DNA. Enzyme: DNA Polymerase I (replaces RNA primers with DNA) 5. DNA fragments are joined together by making the last phosphodiester bond between Okazaki fragments. Enzyme: DNA Ligase (doesn't add any nucleotides, just makes the last phosphodiester bond).

Cytokinesis (Mitosis)

2 diploid daughter cells from mitosis

What purposes do the poly(A) tail and 5'-cap serve?

5' cap: a modified guanine nucleotide Poly (A) tail: 100-250 adenine nucleotides; needed for translation and *protects from degradation* (enzymes "snack"on this instead of the coded mRNA)

Epistasis

A gene masking the expression of another; doesn't express any trait ex. albino mice

polygenic inheritance

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

Primase

An enzyme that joins RNA nucleotides to make the primer.

How does the process of cytokinesis differ between an animal cell and a plant cell?

Animal cells divide by a cleavage furrow. Plant cells divide by a cell plate that eventually becomes the cell wall

S Phase

DNA replication

Explain the process of DNA replication. Be able to put steps in order.

DNA replication 1. HELICASE breaks hydrogen bonds 2. Primer binds as starting point by PRIMASE 3. Elongation by DNA polymerase III (leading strand) in 5' —> 3' 5. Topoisomerase relieves tension 6. Lagging strand has Okazaki fragments 7. Proofreading by DNA polymerase 8. LIGASE joins Okazaki fragments

Central Dogma of Biology

DNA-transcription-RNA-translation-protein

Describe nucleotide excision repair. When is it required?

Damage to one or a few bases of DNA is often fixed by removal (excision) and replacement of the damaged region. In nucleotide excision repair, a patch of nucleotides is removed. used to fix damage from UV radiation, sunburn, smoking. (UV radiation can make cytosine and thymine bases react with neighboring bases that are also Cs or Ts, forming bonds that distort the double helix and cause errors in DNA replication. The most common type of linkage, a thymine dimer, consists of two thymine bases that react with each other and become chemically linked)

How does proofreading of DNA work?

During DNA synthesis, most DNA polymerases "check their work," fixing the majority of mispaired bases. (Mismatch repair happens AFTER replication, proofreading happens DURING replication.)

sexual reproduction: #chromosomes, replication rates, genetic variation, etc

Fertilization introduces variation as haploid sets of chromosomes combine to make unique offspring offspring with unique chromosome complements results in a shuffling of the alleles of the parents into the offspring

Interphase (Mitosis)

G1, S, and G2 phase of cell cycle DNA is replicated in S phase

DNA replication: What proteins are involved?

Helicase Topoisomerase SSBP DNA Polymerase III DNA Polymerase I Ligase

Describe sex linkage and be able to predict patterns of inheritance in the progeny

If a trait appears equally often in males and females, it is likely to be autosomal If males express the trait more often, it is usually X-linked X-linked recessive traits are common Men (XY) will exhibit the trait if they inherit it from their mothers Women (XX) will exhibit the trait only if they are homozygous Usually skips a generation An affected male can pass it only to his daughters Daughters will pass the allele to about half their sons Example: red-green color blindness

What is the role of MPF in mitosis? (M-Phase Promoting Factor)

Induces Mitosis in all eukaryotes (composed of kinase & a cyclin)

Describe each phase of the cell cycle in order. IPMAT (It may help to draw this process out for each phase. Be able to recognize the components and use appropriate language to describe them.)

Interphase Prophase Metaphase Anaphase Telophase

How does splicing occur?

Introns are removed by splicing Catalyzed by small ribonucleoproteins (snRNPs) Done through spliceosome

Single stranded DNA binding proteins (SSBP)

Keeps helix open. (Binds to unwound single stranded DNA and prevent it from reforming a double helix)

When does the law of independent assortment occur?

Metaphase 1

asexual reproduction: #chromosomes, replication rates, genetic variation, etc

Much more efficient / can produce twice as many offspring in the same amount of time No genetic variation

Describe how down syndrome occurs. It is usually due to the sperm or egg?

Nondisjunction. If both homologs or both sister chromatids move to the same pole of the parent cell resulting in aneuploidy (trisomy 21) Usually due to the egg.

What are the differences between prokaryotic and eukaryotic DNA transcription?

Prokaryotic v. Eukaryotic Transcription: Eukaryotic: uses 3 different kinds of RNA polymerase, more diverse, Basal transcription factors instead of sigma proteins, **poly (A) signal, rather than a hairpin structure in prokaryotic, occurs in nucleus

RNA primer (primase)

Provides the 3' hydroxyl group required by DNA Polymerase

Genetic Code Characteristics: (RUNUC)

Redundant Unambiguous (very specific) one codon never codes for more than one amino acid Non-overlapping: codons are read one at a time Universal: all codons specify the same amino acids in all organisms Conservative: if several codons specify the same amino acid, the first two bases are usually identical

What is the difference between sexual and asexual reproduction?

Sexual reproduction: two different genetic gametes. Asexual reproduction: identical copy of parent

DNA Synthesis & dNTPs

Should be endergonic, but enzymes add phosphates to make the reaction exergonic

To become a MATURE mRNA:

Splicing of introns Addition of cap and tail Mature mRNAs contain untranslated regions

Why do deoxyribonucleotides need to be turned into dNTPs for DNA replication to occur?

To create energy.

G 2

Will show replicated chromosomes and centrosomes (from the S phase)

What does "redundancy in the genetic code" mean?

a particular amino acid can be coed for by more than a single codon; Conservative (when the first two base pairs are usually the same)

What is complementary base pairing? Which bases pair together?

adenine - thymine (uracil) guanine - cytosine Each type of nucleotide pairs with only one other type. Hydrogen bonds connect the nucleotide pairs.

Prophase (mitosis)

chromatin condenses into chromosomes centriole pairs separate, move toward opposite sides of the cell, and form spindle fibers made of microtubules the fibers radiate outward from the centrioles nuclear membrane dissolves which allows spindle fibers to contact chromosomes

Telophase (mitosis)

chromosomes begin to uncoil, spindles break down, new nucleur membrane forms.

Metaphase (mitosis)

chromosomes line up on metaphase plate

DNTP

deoxyribonucleotide triphosphate

dNTPs

deoxyribonucleotide triphosphates: free deoxyribonucleotides needed for extension.

DNA ligase

enzyme that chemically links DNA fragments together; seals the Okazaki fragments

How are mistakes in DNA synthesis identified (mismatched pairs)?

enzymes recognize mismatched pair, removes section of incorrect base, fills in with the correct pair. (Mismatch repair happens AFTER replication, proofreading happens DURING replication.)

What human traits are controlled by polygenic inheritance?

height, skin color, eye color and weight.

DNA replication: How is the helix opened and stabilized?

helix is opened by the enzyme helicase, and stabilized by SSBP's and topoisomerase, which relieves the tension.

What roles do the large and small subunits of the ribosome have in translation?

mRNA binds to the small subunit of the ribosome during initiation. Large subunit (with the EPA slots) binds to small subunit.

Where does transcription occur?

nucleus

exception to central dogma

retroviruses

Where does translation take place?

ribosomes in the cytoplasm

start codon (AUG)

signifies the start of the protein-encoding sequence in mRNA

4 types of point mutations (SMNF)

silent, missense, nonsense, frameshift

Anaphase (Mitosis)

sister chromatids separate

Where do nucleotides get added to the nucleic acid?

the 3' carbon (the incoming attaches to the hydroxyl group.)

What role does the p53 gene play if it is intact versus if it is mutated?

tumor suppressor If DNA is physically damaged: - activates proteins that pause the cell cycle until damage can be repaired - Or initiates apoptosis= programmed cell death If the p53 gene is mutated, leads to uncontrolled cell division