BIO 120 Exam #4 Study Guide

DNA as a concept?

DNA has a common structure and functions across life. It's functions are storing of genetic information and copying itself. Nucleotides PURINES have 2 rings, Adenine (A) pairs with Guanine (G). Nucleotides PYRIMIDINES have 1 ring, Thymine (T) pairs with Cytosine (C).

Hydrogen bonds?

A-T have 2 hydrogen bonds, C-G have 3 hydrogen bonds. Hydrogen bonds hold the two nitrogenous bases together across the two strands.

Phosphodiester bonds?

A covalent bond that resists pH and temperature change. This composes the backbone of the DNA strand.

What direction can DNA grow?

DNA grows 5' - 3', DNA polymerase can only be added to the 3' OH end. Phosphodiester bond formation is only possible in this direction. DNA is polar, one side differs from another.

What is base stacking and how do van der waals forces contribute to this?

Interactions between bases on the same strand result in base stacking. Bases are stacked flat on top of each other in the double helix. Van der waals forces contribute to base stacking by helping stabilize the strand.

What are the differences between DNA and RNA?

DNA is a deoxyribose sugar, its bases are A, T, C, G, it is very large, and has a double strand. RNA is a ribose sugar, its bases are A, U, C, G, it is smaller, and has a single strand.

Transcription - how does it work? How is it initiated?

Transcription factors and RNA polymerase bind double-stranded DNA at promoter sequences. It starts at promoter region and ends at terminator region. Prokaryotes do this in the cytoplasm, Eukaryotes do this in the nucleus.

Polymerization reaction - how to add nucleotides?

RNA polymerase II allows for unwinding of the DNA so that complementary nucleotides can be added.

Primary transcript as a conecept?

The primary transcript undergoes a complex process of chemical modifications known as RNA processing. These modifications include: Addition of 5' cap, 5' - 5' bonds provide stability and protection (cap is important to make translation occur). Removal of introns, exons are spliced together so a functional protein can be provided. Addition of poly A tail, targets mRNA and provides protection.

What are the differences between prokaryotes and eukaryotes in primary transcription?

EUKARYOTES have a 5' cap, poly a tail, many introns, splicing, alternative splicing, NO coupling, nucleus-cytoplasm, and long mRNA lifetime. PROKARYOTES have very little introns, coupling, cytoplasm, and a short mRNA lifetime.

Basic structure of amino acids?

Amino acids are the building blocks for protein, all have the same basic core structure.

Hydrophobic R-Groups?

Hydrophobic R groups of amino acids tend to aggregate in the center of proteins away from the aqueous environment found inside and outside of cells (non-polar).

Hydrophilic R-Groups?

Acidic and basic amino acids are strongly polar and hydrophilic. Polar R groups interact with each other and water molecules via hydrogen bonding. Found in outer surface of proteins.

Peptide bonds - what are they and what are they connecting?

Peptide bonds are covalent bonds that join two adjacent amino acids. Occurs during dehydration synthesis reaction, a water molecule is lost.

Four levels of protein folding - what are they? Do they involve the R groups?

Secondary structure, due to hydrogen bonding in the backbone of the polypeptide. Alpha helix, very stable and allows for molecular interactions. Beta sheet, pleated, parallel, or antiparallel, NOT in R groups. Tertiary structure, final folded shape of protein, results in its functional form, final form governed by hydrophilic and hydrophobic groups, secondary structures, and interactions among R groups.

What does it mean when a protein denatures?

It means the unfolding of a protein in response to chemical treatments or high temperatures.

Everything about Translation - how does it work?

tRNA is charged by aminoacyl-tRNA synthetase. Ribosome assembles on mRNA at AUG. Charged tRNAs bring amino acids to ribosome. Peptide bonds form between amino acids (elongation). Ribosome moves along mRNA (translocation). Stop codon reached → release factor releases polypeptide. Ribosome disassembles. A site accepts aminoacyl-tRNA, P site is where peptide bond formation occurs, E site is where tRNA exits ribosome.

What are the three stages of translation?

Initiation, ribosome assembles at start codon and reading frame is established. Elongation, amino acids added one by one and the outcome is a growing polypeptide chain. Termination, stop codon is reached and polypeptide is released, ribosome dissembles.

Cell division and DNA replication: What are the differences between Prokaryotes and Eukaryotes?

Cell division is the process by which cells make more cells. DNA replication ensures genetic continuity. EUKARYOTES have a large genome, DNA is in the nucleus, and nuclear membrane is broken down then restored for complete DNA distribution into each daughter cell. PROKARYOTES have small genome, DNA is in the cytoplasm, and DNA is attached to cell membrane, and cell growth allows for separation into daughter cells.

What is binary fission?

Occurs in prokaryotes, no meiosis or mitosis is involved, efficient for rapid population growth.

What is the eukaryotic cell cycle?

M phase - mitosis and cytokinesis. Interphase, prepares cell to divide in four stages. G1 phase, cell growth and expression of regulatory proteins. S phase, DNA synthesis. G2 phase, preparation for mitosis. G0 phase, cell is not actively dividing.

Linear DNA replication - what are the proteins involved?

Helicase, unwinds the DNA double helix at the replication fork. Single-strand binding proteins, stabilize unwound single strands. Primase, synthesizes short RNA primers to provide a 3'OH group for DNA polymerase. DNA polymerase, synthesizes leading and lagging strand. Telomerase, extends the ends of linear chromosomes to prevent shortening.

What is the lagging and leading strand - why do we see this in linear DNA?

The leading strand has its 3' end pointing toward the replication fork; it is synthesized as one long, continuous polymer as the parental strand is unwound. The lagging strand has its 3' end pointing away from the replication fork; it is synthesized in short, discontinuous pieces.

Why do we have telomeres and telomerase?

The enzymes telomerase can extend the ends of the chromosomes to address chromosome shortening. Telomeres are protective caps.

What is a chromosome?

Contains genetic information in the form of DNA.

What is a sister chromatid?

Identical copy of a chromosome

What is a centromere?

Central point where two chromatids are joined together.

Each of the phases of mitosis?

Prophase, chromatin condenses into visible chromosomes and each chromosome has two sister chromatids, chromosome is condensed. Prometaphase, occurs when microtubules encounter chromosomes and attach to chromosomes at the centromere, condensed. Metaphase, chromosomes align in center of cell, condensed. Anaphase, sister chromatids separate and travel to opposite poles, condensed. Telophase, nuclear envelope reforms and chromosomes decondense. Cytokinesis, cytoplasm divides, forming two daughter cells, chromosomes are fully decondensed in interphase chromatin form.

How many pairs of chromosomes at the start and end?

Start with 46 chromosomes and 92 chromatids. End with 46 chromosomes and 46 chromatids.

What is the difference between Animal and plant cell division?

Mitosis itself is very similar in both. The main differences are in cytokinesis and spindle organization due to structural differences (membrane flexibility and presence of cell wall).

The three Cell Cycle Checkpoints?

DNA damage checkpoint, DNA replication checkpoint, and spindle assembly checkpoint.

What is apoptosis?

Apoptosis dies for the good of the organism, preventing damage to surrounding tissues.

What gene types cause cancer? What is an oncogene, tumor suppressor?

Malignant tumors are cancerous with cells that can spread. Metastasis is the spread of cancer cells. Oncogene is a cancer-causing gene. Proto-oncogenes are normal genes important in cell division that have the potential to become cancerous if mutated. Tumor suppressors encode proteins whose normal activities inhibit cell division.

How does cancer develop from benign to metastatic?

Cancer progression is stepwise, involving accumulation of mutations that allow uncontrolled growth, invasion, and metastasis.

Is cancer on the rise or falling?

Cancer is sadly rising globally.

What are some of the ways to decrease your cancer risk?

Avoid tabbaco and alcohol and increase fruit and vegetable intake.