Bio Exam 2 Studying

First Parity Rule / Chargaff’s Rule

Rule discovered by Chargaff, stating that in a DNA strand %A=%T and %C=%G and that adenine base pairs with thymine and cytosine pairs with guanine

Photo 51 (R. Franklin and R.G. Gosling)

First photo (x-ray diffraction) demonstrating structure of DNA

Watson and Crick

Discovered double-helix structure of DNA

Components of DNA

Phosphate group (negtively charged), 5-carbon deoxyribose sugar, and nitrogenous base (either adenine, thymine, cytosine, or guanine)

Pyrimidines

Cytosine, Thymine, and Uracil (single ring)

Purines

Guanine and Adenine (double ringed)

Nucleotides vs Nucleosides

Nucleotides include all components (phosphate group, sugar, nitrogenous base) and are named adenine, thymine, cytosine, guanine, and uracil, while nucleosides include sugar and nitrogenous base and are named adenosine, guanosine, cytidine, uridine, thymidine

Thymidine Mono-phosphate

Thymine nucleotide

2 vs 3 Hydrogen Bonds

2 Hydrogen bonds form between adenine and thymine while 3 Hydrogen bonds form between guanine and cytosine

5’ to 3’ Orientation

Phosphate group on each nucleotide bonds to the 5’ Carbon of the sugar, so DNA strand is oriented (and built) from the 5’ to 3’ end

Martha Chase & Alfred Hershey

Did experiments with bacteriophages, radio labeling proteins and DNA to track whether targeted cells would inherit each as genetic material, discovery of DNA as genetic material

Differences Between RNA & DNA

RNA: ribose sugar, base uracil with no CH3 group compared to thymine, single stranded; DNA: deoxyribose sugar, base thymine, double stranded

Ribozyme

An RNA molecule that can act enzymatically, such as when splicing RNA (eg tC19Z)

Chromatin Composition

DNA in nucleus of eukaryotes associated with histone proteins, packaging allows DNA to effectively condense, function as genetic information (condenses and decondenses to allow certain areas of DNA to be transcribed), be adjustable to permit tighter or looser coiling

Proteins in Chromatin

Histones: for gene regulation and packaging; Non-histones: enzymes and transcription factors

Woodcock and Ada + Don Olins

Used electron microscopy techniques in order to discover “beads on a string” model of DNA and associated histone proteins (on TEM)

Nucleosome

Also known as a histone octamer or one “bead,” group of 8 histone proteins that DNA wraps around twice connected by linker DNA (string) DNA is negatively charged and the histone proteins are positively charged. 2 of each: H2A, H2B, H3, H4

Gel Electrophoresis - Nucleosome Ladder

Gel electrophoresis of DNA shows discrete units, since nuclease digests linker DNA, displaying the increasing (by integers) ladder structure of nucleosomes

30 nm fiber

Chromatin can coil even more to go from a 10 nm to 30 nm fiber. This process is reversible and different areas of the nuclei can have varying levels of condensing. Can coil even further, and more further during metaphase of mitosis

Homologues

Pair of chromosomes, humans have 22 and sex chromosomes

Replication Fork

Area where bonds between two strands of DNA break to allow each strand to act as a template

Semi-Conservative Replication

During DNA replication, two new strands form with 50% of the old DNA

Meselson and Stahl

Proved that DNA was semi-conservative by using isotopes of Nitrogen to measure density of new strands, found they were both the same density (+tracked second generation)

Leading vs Lagging Strand

Leading strand naturally moves 5’ to 3’ toward replication fork and can therefore add nucleotides freely, lagging strand moves 3’ to 5’ toward replication form so fragments must be done 5’ to 3’ and then linked together (ligated) “Okazaki fragments”

Nucleoside Triphosphate

How new nucleotides enter DNA strand, using energy from other two phosphates to join 3’ end of chain

Origin of Replication

Formation of replication bubbles in eukaryotic DNA that eventually all fuse together. Bacteria only have one bubble

Names for Strands

Template strand: what RNA polymerase reads, also the antisense strand; Coding strand: what mRNA ends up being (with U instead of T), sense strand

RNA Transcription

RNA polymerase binds to the promoter region with general transcription factors (together form basal transcription complex) attaching nucleotides that are complementary to template strand

Primary Transcript

Fresh mRNA strand without any splicing or modifications (before entering cytoplasm)

Mature mRNA

mRNA in cytoplasm after introns (genetic info that does not code for genes) are removed during splicing, leaving only exons (genetic info that codes for genes)

Alternative Splicing

Reason that humans have more proteins that gene-coding regions; idea that exons can be removed from mRNA to form multiple proteins from one gene

Nirenberg, Crick, and Khorana

Solved the universal triplet code (triplet codon to amino acid)

Universal Triplet Code

All domains use the universal triplet code to code for amino acids from a sequence of three nucleotides; the universal triplet code is degenerate, in the sense that multiple triplet codons can code for the same amino acid, and it is also not random as similar triplet codes often code for the same amino acid (if that amino acid has multiple codons)

tRNA

Transfer RNA, carries a specific amino acid to translate mRNA and form a polypeptide chain, contains anticodon for amino acid

Ribosome

Site of translation, where mRNA is read and tRNA’s bind to form polypeptide chain; comprised of a small and large subunit which both contain proteins and rRNA (ribosomal RNA)

tRNA Binding Site

P and A site on large subunit, P site holds tRNA attaching amino acid to polypeptide chain, A site holds next tRNA, tRNA is ejected after and the tRNA in the A site moves to the P site (known as translocation)

Translation Initiation + Termination

Initiation: tRNA with anticodon for Met (start codon AUG), mRNA binds to small subunit, large subunit binds and new tRNA’s bind to A site; Termination: end to elongation after stop codon is read (UAA, UGA, UAG)

Substitution

Mutation where one nucleotide is substituted for another; has the possibility of affecting amino acid (missense), changing amino acid codon to a stop codon (nonsense), or having no effect on the amino acid (silent)

Deletion

Mutation where one or more bases is deleted, typically shifting the frame that RNA polymerase will read (unless deletion is a multiple of three)

Insertion

Mutation where one or more bases is inserted, typically shifting the frame that RNA polymerase will read (unless insertion is a multiple of three)

Mutations Inheritability

Mutations are inherited by one of the two new DNA strands

Functions of Cell Division

Growth via cell development, cell replacement ,and asexual reproduction

Walther Flemming

“The father of cytogenetics,” described the division of the cell nucleus “omnis nucleus e nucleo” (“every nucleus from a nucleus”), first to name Mitosis referring to cell division

Interphase

Cell can be in interphase for short or long periods of time; consists of G1 (cell grows and prepare for S phase), S (replication of DNA in nucleus), and G2 (more growth, prepares cell for division, checks for mutations and damages in DNA) phases

Mitosis

Prophase (chromatin condense, nuclear envelope begins dissolving, spindles start to form), metaphase (chromosomes line up in middle of cell on m plate, spindle fibers attach to each side of the centromere), anaphase (sister chromatids are pulled to opposite poles of cell with spindle fibers (microtubules)), telophase (new nuclear membranes begin forming, spindle dissolves, cleavage furrow forms), and cytokinesis (division of cytoplasm and cell membrane)

Centrosome

Pair of centrioles that go to either side of cell, microtubules grow from which help move chromosomes during mitosis; centrioles have 9 triplets of microtubule proteins

Plant vs Animal Cytokinesis

In plant cells, vesicles containing materials to form cell wall eventually fuse to form a cell plate, dividing the plant cell and forming a cell wall; in animal cells a cleavage furrow divides cells

Sir John Gurdon

First to clone frogs by injecting a frog nucleus into a cell without a nucleus, growing into a tadpole

Transcription Regulation

RNA Can only bind to accessible DNA that is not coiled, and promoters can also attract transcription factors and bind RNA polymerase (increasing transcription rates), repressors can also prevent TFs from binding and therefore the basal transcription complex from forming, while enhancers attract specific TFs and can be more upstream, folding to form basal transcription complex

RNA Processing Regulation

Alternative splicing allows for different proteins to be made from one gene

RNA Export/Stability Regulation

Different mRNA’s have different lifetimes, different mRNAs take a different amount of time to degrade

Translation Regulation

mRNA can be masked to control translation

Protein Stability Regulation

Proteins also have different lifetimes and degrade at different rates

External Cell Signaling Regulation

Cells can receive external signals, potentially activating certain TFs

Adult Stem Cells

Adult stem cells are typically multipotent, meaning they can become different specific, but related tissue cells in different cultures

Embryonic Stem Cells

Embryonic stem cells are pluripotent can develop into several types of cells depending on the culture

Yamanaka

Found that the addition of four specific genes into adult stem cells can make them into induced pluripotent stem cells (iPSCs), having the properties of embryonic stem cells

Chromatin Remodeling

Chromatin can be remodeled with remodeling enzymes to uncoil and open DNA, as it is the template for DNA replication, nucleosome binds to active site of enzyme (using energy from ATP), to unwind DNA from histones to expose it, allowing polymerase and TFs to bind

Acetylation

Introduction of acetyl group causes lysine to lose it’s positive charge attaching to NH3+, helping decondense chromatin (reversible process)

Activator Proteins

Cell-specific enhancer elements that can remodel chromatin to allow polymerase and TFs to bind

Random X Deactivation

It is important for some genes to be turned off, so women’s early cells randomly deactivate one X chromosome known as a Barr Body

MeCP2 Protein

Protein that binds to chromosomes to stop transcription, when mutated it fails to properly allow chromatin condensation and gene silencing, which can lead to Rett Syndrome in females (intellectual disability that kills most men before they are born)

Homoeotic Genes

Master control genes that control the development of body parts in early embryonic development; have been evolutionarily conserved

Gel Electrophoresis

Use of gel matrix to attract negatively charged DNA through “sieve-like” gel, showing smaller fragments that were able to travel further

DNA Hybridization

Treating DNA with heat to disrupt hydrogen bonds between strands (can be reversed by lowering heat), and single strands of DNA can be used to locate genes of interest

Polymerase Chain Reaction (PCR)

DNA sample + sequence-specific ssDNA primers for polymerase + deoxyribonucleotides (A,T,C,G), = + heat resistant DNA Taq polymerase + heat/ATP; primers identify specific regions of DNA that humans are “hyper-varible” in, meaning the DNA sequences are repeated and differ only in length, used to identify people by comparing gel electrophoresis bands

Mary Lyon

Proposed the random deactivation of one X chromosome in female mammals