Glycogen (extensive branching)
a(1-4) branches at a(1-6) animals
amylose (no branching)
a(1-4) plants
Amylopectin (branching)
a(1-4) branches at a(1-6) plants
Exam 3
Cell Cycle
Terminology
Germ Cells - Gamete cells (sex cells/sperm & egg), undergo meiosis, haploid in nature
Somatic Cells - mitotically dividing and Go
-arrest cells, diploid in nature, cells of the body
Diploid/Haploid - 2n is two sets (2n=46 for humans) and n is a single set usually for gametes (n=23 for humans)
Karyotype - arrangement of chromosomes in pairs starting with the longest chromosome (usually in prometaphase)
Allele - alternate forms of genes located on homologous chromosomes
Homologous chromosomes - 2 chromosomes with genes for the same traits (one from each parent)
Autosomes - 22 pairs of chromosomes that do not determine sex
Interphase
G1 Phase
Cell growth, accumulates
materials for DNA synthesis
Subtopic
S Phase
DNA synthesis occurs, and
DNA replication results in
duplicated chromosomes
G2 Phase
Meiosis 1
End product - Four (haploid) genetically different cells with half the chromosomes compared to the beginning (germ cells)
Meiosis 2
Telophase 2 and cytokinesis
Anaphase 2
Metaphase 2
Prophase 2
Same as Mitosis- separation of sister chromatids
Two haploid cells form - each chromosomes still has two sister chromatids
Telophase 1 and cytokinesis
Anaphase 1
Metaphase 1
Prophase 1
Three events unique to meiosis
1) Synapsis and crossing over in prophase 1 (homologous chromosomes physically connect and exchange genetic info
2) Homologous pairs at the metaphase plate
3) Separation of homologs during anaphase 1
A special form of cell division that produces gametes - occurs in reproductive organs - each gamete has one set of autosomes and one sex chromosome
Separation of homologous chromosomes
Mitosis (M phase)
End product - Two genetically identical cells with the same number of chromosomes (somatic cells)
Telephase
1) Spindle fibers disperse
2) Nuclear envelope forms around group of chromosomes at each pole
3) One or more nuecleoli reappear
4) Chromatids - decondense - tangled mass of chromatin - mitosis - division of one nucleus into two nuclei
Cytokinesis
Begins during anaphase and ends after telophase - cytoplasm division
In animals, a cleavage furrow forms from pinching. In plants, a cell plate forms using vesicles.
Anaphase
Shortest phase (sister chromatids move)
1) Separation of sister chromatids are pulled toward opp pole - disjunction
2) Genetic info at two poles is the same
Metaphase
Also known as the "Middle" stage (longest stage)
1) Centrosome at opposite ends
2) Chromosomes align center of cell between poles at 90o angle - metaphase plate
3) Sister chromatids facing opp poles
Prometaphase
1) Degradation of nuclear envelope
2) Microtubules extend from each centrosome and attach to the kinetochore on chromosome
3) Kinetochore of unattached sister chromatid associates w/ other microtubule
4) Two sister chromatids oriented - opp poles (stable arrangement)
Prophase
1) Gradual condensation of chromosomes
2) Sister chromatids
3) Nucleoli begin to break down/disappear
4) Mitotic spindle begins to form
Centrosomes move apart to opp ends
Cell synthesizes proteins
needed for cell division
(two centrosomes, nucleus
envelope seen, one or more
nucleoli
Cell Signaling and Proteins
Proteins and Diffusion
Simple Diffusion
Facilitated Transport
Active Transport (requires protein
Overview of protein functions
1) Transport
2) Enzymes
3) Signal Transduction
4) Cell-Cell Recognition
5) Intercellular Joining
6) Acctachment of cytoskeleton and ECM
Transmembrane, peripheral, and integral proteins
Transduction
Synaptic Signaling
1) Action potential reaches a terminal (first messenger I think)
2) Ca2+ enters neuron (second messenger)
3) Triggers neurotransmitters to be released and taken in by the ligand-gated ion channels on the other neuron
4) Repeats
Overview
1)Reception
2) Transduction (phosphorylation cascade)
3) Response using transcription factor in nucleus
Transduction
1) Adenylyl cyclase turns ATP to cAMP (second messenger)
2) cAMP binds to its first protein kinase, which would add a phosphate group to the next kinase
3) Phophatases removes the phosphate groups from the proteins after use
4) Repeats until the a specific protein is reached and produces a cellular response
After first messenger (signal molecule) binds to GPCR to eventually activate adenylyl cyclase, tranduction occurs
Cell Communication
Ion channel receptor
1) Signal molecule binds to ion channel receptor (ligand-gated for example)
2) Gate opens, letting in ions into the cell for cellular response
3) Eventually, signal molecule unbinds and the gate closes
4) Repeats
Tyrosine Kinase Receptor
1) Two signal molecules bind to tyrosine receptors, causing the two receptors to become a dimer
2) Activated tyrosine-kinase regions become phosphorylated using ATP (unphoshorylated)
3) Fully activated receptor tyrosine-kinase (phosphorylated dimer)
4) Activated relay proteins bind to receptor and create cellular responses
5) Repeats
G-protein coupled receptor
1) Signal molecule binds to receptor and activates it
2) Inactive G-protein binds to receptor and turns GDP to GTP to be active
3) Active G-protein binds to Adenylyl cyclase and activates it
4) Cellular response occurs and inorganic phosphate is removed from G-protein, making it inactive again
5) Back to beginning state
Signal Molecule Receptor
Signal molecule nonpolar/hydrophobic - receptor inside cytoplasm or nucleus (like TESTOSTERONE signaling)
Signal molecule polar/hydrophilic - receptor on the membrane (g-protein linked, tyrosine kinase, ion channel receptors)
Needs second messengers
1) Physical contact (cell touching)
2) Local signaling - releasing a signal (like paracrine or synaptic signaling)
3) Long Distance signaling (hormonal signaling across the body)
Gene expression and Regulation
Cell Cycle Regulation (cancer)
Cancer Cell Traits
Cancer development
1) Polyp - small benign growth
2) Adenoma - larger benign growth
3) Carcinoma - malignant tumor
BRCA 1 and BRCA2 - breast cancer
Tumor-Suppressor Genes - encode proteins that inhibit abnormal cell division
p53 - a transciption factor - if defective or missing, it cannot activate transcription
RAS protein: a type of G-protein that when mutated becomes hyperactive Ras protein, which issues signals on its own
Genes associated with Cancer
Oncogenes (mutated version of proto-oncogene) - cancer-causing genes
Proto-oncogenes - normal genes that code for proteins that stimulate normal cell growth and division
1)Uncontrolled cell growth
2) Accumulation and propagation of mutants
3) Ability to invade and distrupt local and distant tissues
4) Loss of density dependent inhibition and anchorage dependence)
Do not need growth factors to grow and divide (they can make their own growth factor, convey a growth factor signial w/o the actual factor, and have abnormal cell cycle control system
Do not respond normally to body's control mechanisms
Does not have density-dependent inhibition (in which crowded cells stop dividing)
Does not Anchorage dependence (in which cells must be attached to a substratum to divide)
Cell Cycle Regulators
CDK is recycled throughout cell cycle, but cyclin will degrade after M phase.
Cyclin increases from G2 to M and MPF increases w/ it thru M phase
MPF: maturation promoting factor or M-phase promoting factor - G2 to M transition
Cyclin dictates which target protein will be phosphorylated by the CDK - ctrl of cell cycle thru phosphorylating other proteins
CDKs (cyclin-dependent kinases): a kinases that depend upon cyclin (cyclin bound to CDK)
Cyclins: Structureally and functionally related proteins required in cell cycle function in Eukaryotes
Gene Expression
Lac operon (both neg. and pos. regulation) components
Layout:
Promoter -> lacI+ -> Terminator -> Promoter -> Operator -> lacZ+ -> lacY+ -> lacA+ -> Terminator
LacI+ is always ON and making high levels of mRNA - which means it is constitutive
Structural genes: lacZ (beta-galactosidase - turns lactose into galactose and glucose), lacY (permease - opens the cell to allow lactose to come in), and lacA (transacetylase - adds an acetyl group to lactose or any other molecule)
Lac Operon ON only when lactose is present
Lac Operon OFF when glucose is present or if there is an absense of lactose
Trp Operon (looks very similar to lac operon and is a form of neg. regulation)
Trptophan present = trp operon off
Trptophan absent = trp operon on
Positive Regulation - Activator bound to operator = transcription / activator not bound = no transcription
Negative Regulation - Repressor not bound to operator = transcription / repressor bound to operator = no transcription
Operons - A cluster of functionally related genes can be under a coordinated control of a single on-off "switch
"Switch" is a segment of DNA called an Operator, which is usually in the promoter
Enchancers are the switch in Eukaryotes
Regulation of Gene expression in Prokaryotes - Operons
Gene regulatikon in Euk
Combinatorial control of gene expression - basically you need to have to specific available activators bound to the enchancers in order to express a gene
Example: In a liver cell, Albumin gene is expressed b/c it has the necessary activators on the enhancers, but it doesn't express crystallin (in the eye) b/c there aren't any activators present for it
Transcription Factors - present inside the nucleus, waiting to be active
General Transcription Factors - leads to low (basal level of transcription)
Specific Transcription Factors - activators (lead to increased expression or high lvl) and repressors (leads to low or basal lvl of expression)
Control Sequences in DNA
Proximal control elements: Sequences in DNA close to promoter
Distal control elements: Sequences in DNA upstream or downstream of gene - may even be located in an intron
ex. Enchancers
Expression
Heterochromatin: highly compact / no genes expressed
Euchromatin: Less compaction / genes expressed
Differential gene expression - Human cell expresses 20% of genes at a time and genes expressed in different cells are different
DNA Packaging
10-nm fiber: DNA winds around histones to form nucleosome "beads" / strung together using linker DNA
Histones - beads on a string (DNA wraps around it twice - histones used: H1, H2A, H2B, H3, H4
Translation
Peptidyl Transferase
enzyme takes the amino acid and adds it to the existing polypeptide chain
ribosomal RNA
where the elongation of the polypeptide occurs. Consists of a small subunit and a large submit. Made of RNA and proteins
Aminoacyl-TRNA synthesase
enzyme responsible for matching the correcting amino acid with a tRNA
Anticodon
nucleotide bases complimentary to the coding mrna strand
tRNA
translates mrna sequence using the triplet code
DNA Repliclation
DNA polymerase
DNA polymerase 3
elongates the RNA primer 5' to 3' by writing complimentary DNA
DNA polymerase 1
enzyme that removes RNA primer and replaces them with DNA nucleotides
Lagging Strand
made of Okazaki fragments, made discontinously
Leading Strand
made 5' to 3' continuously, uses one primer and DNA polymerase 3 elongates
Ligase
joins Okazaki fragments together
Primase
starts an RNA chain complimentary to DNA strand , makes multiple one at a time
Single Stranded Binding Protein
binds to the unwinded strands to prevent the rebinding of them
Topoisomerase
enzymes that relieves stress at the ends of unwound strands to reduce
Helicase
unwinds DNA
Replication Fork
Y shaped region found in both directions of DNA replication after DNA is unwounded
Primer
Nucleotide sequence produced first in DNA synthesis made of RNA
ORI
Replication of DNA starts here
Exam 1
Molecules
Carbon Skeletons
Double Bonds
Rings
Brancing
Chains- Long and short
NEED TO MEMORIZE- Hydroxyl (OH), Carbonyl (CO), Carboxyl (COOH), Amino (NH2), Sulfhydryl (SH), Phosphate (PO3), Methyl (CH3)
Macro-molecules
Nucleic Acids
Nucleotide- with phosphate
Cytosine
Thymine
Adanine
Guanine
Nucleoside- no phoshate
DNA- (the sugar lacks an oxygen)
RNA
Proteins
Side chain
R group
Main chain
N,C,H terminus
quaternary- combination of tertiary (dimer)
tertiary- interactions of R groups
secondary- interactions of N, C terminus
primary- order of amino acids
Fats
Amphipathic
Steroids
HDL good LDL bad
Micelles- used in
phospholipids
Glycerol
Hydrocarbons
Unsaturated fats
Less hydrogen
Saturated fats
More hydrogen
Bad for your body
Carbohydrates
Glucose
Beta (OH up)
Apha
(OH down)
Monosaccarhide
(Di/poly)saccarhides
Polysaccharides
Starch (alpha)
OH on bottom
Cellulose (beta)
OH alternating
b(1-4) plants
Sucrose- Glucose+Fructose
Maltose- Glucose 2x
Biology
Exam 2
Transcription
Exons
coding segments of nucleotides that are later expressed into amino acids
Introns
non-coding segments of nucleotides that lie between exons (coding regions)
Spliciesomes
proteins responsible for splicing RNA
Transcription Factors
proteins that help with the binding of RNA
polymerase to the promoter to initiate transcription
RNA Splicing
the pre-mrna strand is spliced: exons stay in and introns are spliced out
Transcription Initiation Complex
complex of transcription factors and RNA pol 2 bound to the the promoter
RNA Processing
a 5' cap and 3' tail is added to the RNA transcript
Terminator
this sequence signals the end of transcription
Promoter
RNA pol attaches her and starts transcription
TATA Box
the sequence of DNA where the initiation complex forms in eukaryotes
RNA Polymerase
separates two strand of DNA and joins
complimentary RNA nucleotides together to form the RNA strand
Basic Chemistry
pH Scale
Opposite of the pOH scale
-log[H+]
10^x = x is the pH level
Strength order L --> G Van der Waals, hydrophobic, hydrogen, Ionic, Covalent
Isomers
Enantiomers- Mirror images of eachother
Geometric- Same geometric structure but different spacial configurations
Trans-isomer- similar molecules are on different sides
Cis-isomer- similar molecules are on the same side
Structural- same chemical formula, but different arrangement of atoms
Bonds
Ionic- e- taken
Na+ Cl-
Covalent- e- shared
Nonpolar
C-C , O-O , C-H
Polar
Water (H2O) Emergent properties
Universal solvent
Hydration shell
Denser as a liquid
Exhibits temporary hydrogen bonding
Expands when a solid
Exhibits permanent hydrogen bonding and a lattice structure
High specific heat
Heat of vaporization (high)
When water evaporates it releases heat
Regulates temp well
Cohesion and adhesion behavior
High surface tension for bugs to walk on water
Water transport up trees
O-H , O-C , N-H
Interactions
Dipole-Dipole
Ion-diple
Hydro "phobic" and "philic"
Van der waal's
Hydrogen Bonds
