Biology Hidden Gems Must Memorize Flashcards
Fatty Acids
Building blocks for most but not all complex lipids.
Long chains of carbon truncated on one end by COOH.
Can be Saturated or Unsaturated (by hydrogens)
Triacylglycerols
Store Metabolic energy, provide insulation and padding.
Sometimes called triglycerides or simple fats and oils
Constructed from a three carbon backbone named glycerol
Adipocytes
Fat cells that are specialized cells where their cytoplasm contains nothing but triglycerides
Phospholipids
Serve as a constructional component of membranes.
Built from a glycerol backbone but a polar phosphate group replaces one of the fatty acids.
Amphipathic-have two charges on two different sides of the molecule.
Steroids
Four ringed structures including hormones, vitamin D, and cholesterol (a vital membrane component)
Regulate metabolic activities
Lipoproteins
Transfer lipids that are insoluble in aqueous solution
Contains a lipid core surrounded by phospholipids and apoproteins
Classified by their density. VLDL, LDL, HDL
Proteins (Polypeptides)
Built from a chain of amino acids held together by peptide bonds
Important Amino Acids
Proline-disrupts alpha-helices
Alanine-a methyl group
Glycine-just a hydrogen
Cysteine/Methionine- both contain a sulfur
Both alpha helices and beta sheets reinforced by hydrogen bonds between the carbonyl oxygen and the hydrogen on the amino group.
Five Forces Create tertiary structure
Covalent disulfide bonds between two cysteine amino acids on different parts of the chain.
Electrostatic (ionic bonds): Mostly between acidic and basic side chains
Hydrogen Bonds
Van der Wals forces
Hydrophobic side chains pushed away from water towards the center of the protein.
When you see Nitrogen THINK…
Protein
Glycoproteins
Proteins with carbohydrate groups attached
Proteoglycans
Mixture of proteins and carbohydrates
Anomers
-Alpha- When the hydroxyl group on the first carbon and the methoxy group on the 6-carbon are on opposite sides.
Glycogen
- Found in all animal cells, large amounts found in muscle and liver.
- Liver regulates blood glucose levels so they are one of the few cell types capable of reforming glucose from glycogen and releasing it back into the blood stream.
- Only certain epithelial cells in the digestive tract and the proximal tubule of the kidney are capable of absorbing glucose against a concentration gradient. This is done via secondary transport down the sodium concentration gradient.
Insulin
Increases the rate of facilitated diffusion for glucose and other monosaccharides.
In the absence of insulin only neural and hepatic cells are capable of absorbing sufficient amounts of glucose via the facilitated transport system.
Minerals
DIssolved inorganic ions inside and outside the cell. By creating electrochemical gradients they assist in the transport of stuff into and out of the cell.
Enzyme Models
Lock and Key- the active site of the enzyme has a specific shape that only binds the specific substrate
Induced fit model-The shape of both the enzyme and the substrate are altered upon binding
Enzyme Kinematics
Vmax is proportional to enzyme concentration
Km does not vary with enzyme concentration and therefore is a good indicator of an enzyme’s affinity for its substrate
Cofactor
non-protein component required by an enzyme to reach the optimal activity; either mineral or coenzyme
Apoenzyme
An enzyme without its cofactor
Coenzyme
Cosubstrates and prosthetic groups
Cosubstrates
Reversibly bind to a specific enzyme and transfer some chemical group to another substrate. The cosubstrate is then changed back to it’s original form by another enzymatic reaction
Prosthetic groups
Remain covalently bound to the enzyme throughout the reaction
Competitive inhibition
Raise the apparent Km but do not change the Vmax
Can be overcome by excess substrate
Noncompetitive inhibition
Can’t be overcome by excess substrate
Vmax is lowered but since enzyme affinity is the same Km remains the same
Vmax
The rate of reaction when the enzyme is saturated with substrate is the maximum rate of reaction,
Vmax is the reaction rate when the enzyme is fully saturated by substrate, indicating that all the binding sites are being constantly reoccupied
Km
Km is the concentration of substrate which permits the enzyme to achieve half Vmax. An enzyme with a high Km has a low affinity for its substrate, and requires a greater concentration of substrate to achieve Vmax
Uncompetitive Inhibition
Uncompetitive inhibition, also known as anti-competitive inhibition, takes place when an enzyme inhibitor binds only to the complex formed between the enzyme and the substrate (the E-S complex). Uncompetitive inhibition typically occurs in reactions with two or more substrates or products.
Km reduced and Vmax reduced
Line weaver Burke plots for inhibition
Feedback inhibitors do not resemble…
The substrate of the enzyme they inhibit
Allosteric regulation
Come back and bind to a different site of the enzyme causing a conformational change, many alter affinity of substrate for enzyme (Km) but not Vmax.
Can be either positive or negative regulation
At low substrate concentrations, small increases in substrate concentration increase enzyme efficiency as well as reaction rate.
Lyase
Catalyzes the addition of one substrate to a double bond while a ligase governs an addition reaction using ATP.
Metabolism
1) Macromolecules are broken down into their constituent parts releasing little or no energy
2) Constituent parts are oxidized to acetyl CoA, pyruvate or other metabolites forming ATP and reduced enzymes (NADH and FADH2)
3) If oxygen is available and the cell is capable of using oxygen these metabolites go into the citric acid cycle and oxidative phosphorylation to form large amounts of energy (more NADH, FADH2, or ATP); otherwise the coenzyme NAD+ and other byproducts are either recycled or expelled as waste.
Glycolysis
First step of anaerobic and aerobic respiration
- Starting molecule is glucose
- Products: 2 molecules of ATP from ADP/water, 2 pyruvate molecules from 1 glucose, 2 molecules of NADH from reduction of NAD+
- In the third step the molecule is committed to glycolysis
- Regulated and committed steps are 1,3,10. Very - delta G. Very spontaneous
Substrate level phosphorylation
The formation of ATP from ADP using energy from the decay of high energy phosphorylated compounds as opposed to using energy from diffusion (oxidative phosphorylation)
-2 ATPs are spent, 4 ATPs are produced
Much of the fructose and galactose ingested by humans is converted into glucose in the liver enterocytes; however fructose can enter as
fructose-6-phosphate or G3P; galactose can be converted to G6P to enter glycolysis.
Fermentation
- Anaerobic respiration
- Includes glycolysis, reduction of pyruvate to ethanol or lactic acid, and oxidation of NADH back to NAD+
- Takes place when a cell or organism is either unstable to assimilate the energy from NADH and pyruvate, or has no oxygen available to do so
- Recycles NADH back to NAD+
Aerobic Respiration
- Products of glycolysis move into the matric of the mitochondrion
- Once inside the matrix, pyruvate is converted to acetyl CoA in a reaction that produces NADH and CO2
Krebs Cycle
- Acetyl CoA transfer two carbons from pyruvate to 4-carbon oxaloacetic acid
- Each turn produces 1 ATP, 3 NADH, and 1 FADH2
- ATP production in the Krebs cycle is substrate-level phosphorylation
- Triglycerides can also be catabolized for ATP. Fatty acids are converted into acyl CoA along the outer membrane of the mitochondrion and endoplasmic reticulum at the expense of 1 ATP.
- The reaction also produces FADH2 and NADH for every two carbons taken from the original fatty acid
- The glycerol backbone is converted to PGAL
Amino acids are deaminated by…
the liver. The deaminated product is either chemically converted to pyruvic acid or acetyl CoA, or it may enter the Krebs cycle at various stages depending upon which amino acid was deaminated.
Electron Transport Chain
- A series of proteins on the inner membrane of the mitochondrion
- The first protein complex in the series oxidizes NADH by accepting high energy electrons that it will then pass to O2
- As electrons are passed along, protons are pumped into the intermembrane space for each NADH
- The protons then diffuse back to the mitochondrial matrix turning ADP into ATP through the pump, ATP synthase
Oxidative phosphorylation-production of ATP through diffusion/oxidation of NADH, like this
Intermembrane space has lower pH than matrix. (More acidic because of all the protons being pumped out into it.
Aerobic respiration produces how many net ATPs?
About 36 net
How many ATP does 1 NADH bring back?
2 to 3 ATPs
How many ATP does 1 FADH2 bring back?
2 ATPs
Glucose + O2—–>
CO2+H2O
Not balanced here, its a combustion reaction
Gene
Series of nucleotides that code for the production of a single polypeptide or mRNA, rRNA, tRNA
Eukaryotes can have multiple copies or a gene but prokaryotes only have one copy of each gene.
Eukaryotic genes that are actively transcribed by a cell area associated with regions called
Euchromatin
Genes not being actively transcribed are associated with tightly packed regions called
Heterochromatin
Genome
Entire sequence of DNA of an organism
Central Dogma
DNA is transcribed to RNA, which is translated to amino acids forming a protein
DNA
Sugar phosphate backbone
Phosphodiester bond
3’ end attached to an -OH group and 5’ end attached to a phosphate group
A2T hydrogen bonds, C3G hydrogen bonds
Semi Conservative DNA replication
When a new strand is created one strand from the original DNA goes to the new strand.
What is DNA replication governed by?
Replisome.
Two replisomes proceed in opposite directions along the chromosome making replication a bidirectional process.
The point where a replisome is attached to the chromosome is called the replication fork.
Replicons
Replication units- each chromosome of eukaryotic DNA is replicated in many discrete segments called replicons.
DNA helicase
Unwinds double helix
DNA polymerase
Enzyme that builds the new DNA strand, can’t initiate a strand from two nucleotides, needs primer
Reads from 3’—> 5’ (upstream direction), writes 5’—>3’ (downstream)
Primase
-an RNA polymerase creates an RNA primer 10 ribonucleotides long to initiate the strand
Lagging strand
Interrupted strand
Made up of Okazaki Fragments
Leading Strand
Written Continuously
Since the formation of one strand is continuous and the other fragmented, the process of replication is called semi discontinuous
DNA ligase
Moves along lagging strand and ties the Okazaki fragments together
Exonuclease
Removes nucleotides from the center of strand, exonuclease on DNA polymerase
Telomeres
Repeated six nucleotide units that protect the chromosomes from being eroded through repeated rounds of replication
Telomerase
Catalyzes the lengthening of telomeres
Differences between DNA and RNA
RNA is produced by transcription-RNA is manufactured from a DNA template in this process
-DNA is produced by replication
rRNA (ribosomal RNA)
Combines with proteins to form ribosomes
Initiation
Beginning of transcription
- An initiation factor finds a promoter on the DNA strand
- Promoter- sequence of DNA nucleotides that designates a beginning point for transcription
In prokaryotes its located upstream
Most commonly found sequence is the consensus sequence
Variations from the consensus sequence causes RNA polymerase to bond less tightly and less often leading to those genes being transcribed less often.
After binding to the promoter RNA polymerase unzips the double helix creating a transcription bubble, next the complex switches to elongation mode
Elongation
RNA polymerase transcribes only one strand or antisense strand.
The other strand, the sense strand (coding strand) protects its partner against degradation
RNA polymerase moves along the DNA strand from 3’—>5’ building the new RNA 5’—>3’. NO proofreading, 10X slower than replication
Termination
Requires special termination sequence to tell RNA polymerase to detach.
- Replication makes no distinction between genes, transcription does through activators and repressors
- Most genetic regulation occurs at transcription when regulatory proteins bind DNA and activate or inactivate its transcription.
Activators and Repressors
Bind to DNA close to the promoter and either activate or repress the activity of RNA polymerase (activators before the promoter sequence, repressor after)
- Primary function of gene regulation in prokaryotes is to respond to environmental changes
- Changes in gene activity are a response to the concentration of specific nutrients in and around the cell
- Primary function of gene regulation in multicellular organisms is to control intracellular and extracellular environments
Polycistronic
Prokaryotic mRNA typically includes several genes in a single transcript
Monocistronic
Eukaryotic mRNA includes one gene per transcript
Operon
Genetic unit of prokaryotic DNA consisting of the operator, promoter and all other genes that contribute to a single mRNA
Post-transcriptional Processing
Occurs in both eukaryotes and prokaryotes
-In prokaryotes rRNA and tRNA go through post-transcriptional processing but mRNA usually doesn’t
in eukaryotes mRNA goes through post-transcriptional processing too
Primary Transcript
initial mRNA nucleotide, also known as pre-mRNA
- Processed in three ways
1. Addition of nucleotides
2. Deletion of nucleotides
3. Modification of nitrogenous bases
In eukaryotic mRNA the 5’ cap is added as protection against degradation by exonucleases
The 3’ end is polyadenylated with a poly A tail to protect it from exonucleases
Introns
Before leaving the nucleus, introns are removed from the pre-mRNA
Do not code for protein and are degraded in the nucleus
Exons
Parts of pre-mRNA that survive post-transcriptional processing
-can be spliced together in different ways to code for different proteins
snRPs
Recognize nucleotide sequences at the ends of introns
- Several snRPs form a complex called a spliceosome
- Spliceosome-inside introns are looped bringing exons together
Denatured
When heated or immersed in high concentration salt solution or high pH solution
Melting temperature Tm is higher for G-C because they make more hydrogen bonds than A-T
Denatured DNA is less viscous, denser, and more able to absorb UV light
Nucleic Acid Hybridization
Separated strands like to spontaneously associate with their original parter: DNA-DNA, DNA-RNA, RNA-RNA
Restriction enzymes (endonucleases)
Digest (cut) nucleic acid sequences
bacteria defend themselves from viruses by cutting the viral DNA into fragments
Bacteria protect their own DNA with methylation (adding -CH3)
Typically a restriction site is palindromic
Recombinant DNA
DNA that is reformed from restriction endonuclease cuts (remember sticky ends)
Reconnected by DNA Ligase
Can be made long enough for bacteria to replicate and then placed within the bacteria using a vector, typically a plasmid or sometimes a virus
-The bacteria can then begin to be grown in large quantity forming a clone of cells containing the vector with the recombinant DNA. The clones can be saved in a library.
By including in the vector a gene for resistance to a certain antibiotic and the lacZ gene which enable the bacteria to metabolize the sugar X-Gal
When you apply the antibiotic those without the vector will die
You use an endonuclease that cuts at the lacZ gene to insert the new DNA so if the bacteria metabolizes X-Gal you know its not the right bacteria. Clones with the active lacZ gene turn blue.
Complementary DNA (cDNA)
DNA reverse transcribed from mRNA
-It’s useful to clone DNA with no introns so you use reverse transcriptase
Polymerase Chain Reaction
The double strand to be cloned(amplified) is placed in a mixture with primers, polymeraseHeated to 95°C to denature it, cooled to 60°C, the primers hybridize(anneal) to their complementary ends of the DNA strands–Heat resistant polymerase is added and is activated when the temperature hits 72°C
Southern Blotting
- technique to identify target fragments of known DNA sequence in large populations
- DNA is cleaved into restriction fragments which are then resolved by gel electrophoresis
- Large fragments move slower than small ones
Next, the gel is made alkaline to denature the DNA and a sheet of nitrocellulose is used to blot the gel which transfers the resolved single stranded DNA fragments onto the membrane
-A radio labeled probe with a nucleotide sequence complementary to the target fragment hybridizes with and marks the target fragment…this reveals the location of the probe and the target fragment.
Northern Blotting
Just like southern blotting except it identifies RNA
Western Blot
Can detect a particular protein in a mix of proteins
- First the mixture of proteins is resolved by size through electrophoresis
- Next they are blotted onto a nitrocellulose membrane
An antibody(the primary antibody) specific to the protein in question is then added and binds to that protein. Next, a secondary antibody-enzyme conjugate is added and binds to that protein
-The secondary antibody recognizes and binds to the primary antibody and marks it with the enzyme for subsequent visualization. The reaction catalyzed by the enzyme attached to the secondary antibody can produce a colored, fluorescent or radioactive reaction product which can be visualized with an x-ray film
Restriction Fragment Length Polymorphisms (RFLP)
- Identifies individuals as opposed to specific genes
- People possess different restriction sites and varying distances between them
DNA is…
Degenerative, unambiguous and almost universal
Start Codon
AUG
Stop codons
UAA, UAG, UGA
RNA is written
5’—>3’
Translation
Process of protein synthesis directed by mRNA
Ribosome
Prokaryote 30s and 50s form 70s
Eukaryote 40s and 60s form 80s
-Formed in a special organelle called the nucleolus (prokaryotes don’t have these)
After post transcriptional processing mRNA leaves the nucleus through the nuclear pores and enters the
cytosol
The 5’ end of mRNA attaches to the
small subunit of a ribosome
A tRNA with 5’-CAU-3’ (AUG start codon) gets methionine and puts it in the P site
This signals the large subunit to attach and form the initiation complex
This is called initiation
Elongation
A tRNA with its corresponding AA attaches to the A site at the expense of 2 GTP’s
-The C-terminus of the methionine attaches to the N-terminus of the amino acid.
Translocation
- The term for the ribosome shift 3 nucleotides closer to the 3’ end
- The tRNA carrying methionine moves to the E site where it can exit the ribosome and the dipeptide moves to the P site so the A site is free for the next tRNA
- Ends when a stop (nonsense) codon reaches the A site, then an H2O is added to the end of the polypeptide chain
- Even as the polypeptide is being synthesized it begins folding, assisted by chaperones.
Post translational modifications
Sugars, lipids, or phosphate groups can be added to amino acids
-Polypeptide can be cleaved in many places
Where does translation take place?
On a free floating ribosome in the cytosol or it may attach itself to the rough ER during translation to inject proteins in the ER lumen.
- Proteins injected into the ER lumen become membrane bound proteins of the nuclear envelope, ER, Golgi, lysosomes, plasma membrane, or will be secreted from the cell
- The growing polypeptide itself may or may not cause the ribosome to attach to the Er depending upon the polypeptide
Signal Peptide
20 aa sequence that is recognized by a protein-RNA signal recognition particle (SRP)
SRP carries the entire ribosome complex to a receptor protein on the ER where it is removed by an enzyme
Can also attach to polypeptides to target them to mitochondria, nucleus, or other organelles.
Gene mutation
Mutation to a single gene
Chromosomal mutation
Occurs when the structure of the chromosome is changed
Mutagen
Chemical agent that causes mutations
Point Mutation
Mutation that changes a single base pair of nucleotides in a double strand of DNA
Base pair substitution
Where one base pair is replaced by another
Missense mutation
Base pair mutation that occurs in the amino acid coding sequence of a protein; may or may not alter the amino acid sequence of the protein (degeneracy)
-May or may not alter the AA sequence of the protein
If no change in its function it’s a neutral mutation, if an AA isn’t changed it’s a silent mutation
Insertion or deletion
May or may not result in a frameshift mutation
Frameshift mutation
Results when insertions or deletions occur in groups of 3
Nonsense Mutation
When an insertion or deletion results in a stop codon
Chromosomal Mutations
May occur to a chromosome in the form of deletions, duplications, translocations, and inversions
-Deletions occur when a portion of the chromosome breaks off or it lost during recombination/crossing over
Duplications-when a DNA fragment breaks free of one chromosome and incorporates it into a homologous chromosome
Translocation
When a segment of DNA from one chromosome is inserted into another chromosome
Inversion
When a segment of DNA is reversed
Transposable elements/ transposons
Can excise themselves from a chromosome and reinsert themselves at another location
- Will be flanked by identical sequences
- One way an organism can modify its genetic makeup without meosis
Wild type
Original state
Proto Oncogenes
Stimulate normal growth of cells; can be converted to oncogenes that cause cancer by mutagens
Histones
Sections of DNA that are not in use are wrapped around proteins called histones.
8 histones wrapped in DNA form a nucleosome which wrap into coils called solenoids, which wrap into super coils
Basicity of a histone gives them a net positive charge at normal pH of the cell
Chromatin
the total DNA/ protein complex
Constitutive Heterochromatin
Chromatin that is permanently coiled
Euchromatin
Only coiled during nuclear division
How many chromosomes are there?
- In the nucleus of a human somatic cell there are 46 double stranded DNA molecules
- There are 46 chromosomes before replication, and 46 chromosomes after replications
- That means 23 pairs
- Duplicates can be referred to separately as sister chromatids
Homologues
Each chromosome possesses a partner that codes for the same traits as itself
Diploid
Any cell that contains homologous pairs
Haploid
Any cell that does not contain homologous pairs
Four stages of Cell life cycle
G1-first growth phase
S-Synthesis
G2-Second growth phase
M-Mitosis or Meiosis
C-Cytokinesis
Interphase=G1,S,G2
G1 Phase
The cell has just split and begins to grow in size making new organelles and proteins
- Regions of chromatin have been unwound and decondensed into euchromatin
- RNA and protein synthesis is very active
- The cell has to reach a certain size and synthesize sufficient protein to continue to the next stage
Cell growth is accessed at the G1 Checkpoint near the end of G1
Normally the longest phase
G1 Checkpoint
If conditions are favorable the cell center the S phase; otherwise it enters the G0 phase
-Main factor in triggering the beginning of S is cell size based upon ration of cytoplasm to DNA
G0
The non growing phase distinct from interphase
Allows for the differences in length of the cell cycle
S phase
In this phase the cell devotes most of its energy to replicating DNA
- Organelles and proteins are produced more slowly
- Each chromosome is exactly duplicated but, by convention, the cell is considered to have the same number of chromosomes just now each chromosome is made of two identical sister chromatids
G2 Phase
The cell prepares to divide
Organelles continue to duplicate
RNA and protein (especially tubulin for microtubules) are actively synthesized
Occupies 10-20% of the cell cycle
Near the end of G2 is the G2 checkpoint
G2 checkpoint
Checks for the mitosis promoting factor (MPF) If enough MPF mitosis is triggered
Mitosis
Nuclear Division WITHOUT genetic change
4 stages: PMAT
Prophase
- Condensation of chromatin into chromosomes
- Centrioles move to opposite ends of the cell
- First the nucleolus and then the nucleus disappears; the spindle apparatus begins to form consisting of aster (microtubules radiating from the centrioles), kinetochore microtubules growing from the centromeres (a group of proteins near the center of the chromosome), and spindle microtubules connecting the two centrioles.
Kinetochore
The structure of protein and DNA located at the centromere of the joined chromatids of each chromosome
Metaphase
Chromosomes line up along the equator of the cell
Anaphase
Begins when sister chromatids split at their attaching centromeres and move toward opposite ends of the cell (disjunction)
Cytokinesis
Actual separation of the cytoplasm due to constriction of the microfilaments about the center of the cell; indicates the end of anaphase
Telophase
Nuclear membrane reforms followed by reformation of the nucleolus. Chromosomes decondense and become difficult to see under the light microscope
Meiosis
- Double nuclear division which produces four haploid gametes (germ cells)
- In humans only the spermatogonium and the oogonium undergo meiosis
- After replication happens in the S phase of interphase the cell is called a primary spermatocyte or primary oocyte
- In females replication takes place before birth and the life cycle of all gametes are arrested at the primary oocyte stage until puberty
- Just before ovulation, a primary oocyte undergoes the first meiotic division to become a secondary oocyte
- The secondary oocyte is released upon ovulation and the penetration of the secondary oocyte by the sperm stimulates anaphase 2of the second meiotic division in the oocyte.
- Meiosis is two rounds of cell division called meiosis 1 and meiosis 2
Meiosis 1
same as mitosis except for a few differences
- Prophase 1- homologous chromosomes line up along side each other matching genes exactly; at this time they can exchange DNA by crossing over.
- Genetic recombination occurs during crossing over
- Each duplicated chromosome in prophase 1 appears as an X; the side by side homologues exhibit a total of four chromatids known as tetrads.
- If crossing over does occur, the two chromosomes are zipped along each other where nucleotides are exchanged forming the synaptonemal complex.
Synaptonemal complex
is the single point where the two chromosomes attach creating the x shape known as the chiasma
Genes that are located next to each other are said to be
Linked
Chromosome Counts
Meiosis is like mitosis except that in meiosis
there are two rounds, the daughter cells are haploid, and genetic recombination occurs. Recognize that metaphase in mitosis would appear like metaphase 2 in meiosis and not like metaphase 1
Metaphase 1
In metaphase 1 the homologues remain attached and move to the metaphase plate.
Instead of single chromosomes aligned along the plate in mitosis tetrads align in meiosis.
Anaphase 1
Separates homologues from their partners
Telophase 1
A nuclear membrane may or may not reform and cytokinesis may or may not occur.
In humans the nuclear membrane does not reform and cytokinesis doesn’t happen.
If cytokinesis occurs, the new cells are haploid with 23 replicated chromosomes and are called secondary spermatocytes or secondary oocytes. For the female one of the oocytes called the first polar body is much smaller and degenerates. This is to conserve cytoplasm which is only contributed by the ovum. The first polar body may or may not go through meiosis 2 producing two polar bodies.
Meiosis 1 is
reduction driven
Meiosis 2
- Proceeds with prophase 2, metaphase 2, anaphase 2, and telophase 2 and appears under the microscope to be similar to mitosis
- Final products are haploid gametes with 23 chromosomes
- For the spermatocyte 4 sperm cells are formed, for the oocyte a single ovum is formed.
In females telophase 2 produces one gamete and a second polar body
Nondisjunction
- if during anaphase 1 or 2 the centromere of any chromosome doesn’t split
- Nondisjunction in anaphase 1 results in one of the cells will have two extra chromatids (a complete extra chromosome) and the other will be missing a chromosome. The extra chromosome will line up along the metaphase plate and behave normally in metaphase 2.
- Nondisjunction in anaphase 2 will result in one cell having one extra chromatid and one lacking one chromatid.
- Can also occur in mitosis but ramifications are less severe because genetic info in new cells isn’t passed over to new cells.
Viruses
Capsid, nucleic acid, and lipid-rich protein envelope
For some viruses: tail, base plate, and tail fibers for most bacteriophages
Capsid
Protein coat of a virus.
One to several hundred genes in the form of DNA or RNA inside the capsid inside–viruses contain either DNA or RNA exclusively.
Envelope
-Most viruses surround themselves with a lipid rich envelope either borrowed from the membrane of the host cell or synthesized in the host cell cytoplasm.
Contains virus-specific proteins.
Virion
Mature virus outside the cell
Why are viruses not alive?
- can reproduce but always need host cells machinery
- Don’t metabolize organic nutrients; use ATP of host cell
- In their active form they aren’t separated from their external environment by a barrier like a cell wall or membrane
- Possess either DNA or RNA-all other living organisms contain both
- can be crystallized without losing their ability to infect
How does a virus infect?
Infection begins when virus absorbs to a specific chemical receptor site on the host (usually a specific glycoprotein)
Next, the nucleic acid of the virus penetrates into the cell
Bacteriophage
A virus that infects bacteria.
Nucleic acid is normally injected through their tail after viral enzymes have digested a hole in the cell wall.
This means viruses have digestive enzymes
Endocytotic
Most viruses that infect eukaryotes are engulfed like this
Lytic Infection
- When a virus takes over the cell’s machinery to reproduce new viruses
- Eclipse period: the brief period before the first fully formed virion appears
- Latent period-period from infection to lysis
- Virulent Virus-a virus that follows the lytic cycle
Lysogenic infection
- Viral DNA is incorporated into host genome
- Reverse transcriptase-if the virus is an RNA virus and it possesses this enzyme DNA is reverse transcribed. When the host replicates this DNA does as well
- Temperate virus- virus in the lysogenic phase
Provirus-when a virus is dormant or latent
- A prophage if the host cell is a bacterium
- Dormant viruses can become active when there is a stress on the cell such as UV radiation or carcinogens
Plus Strand RNA
indicates that protein can be directly translated from the RNA
Retrovirus-carries the enzyme reverse transcriptase to create DNA from RNA
Minus strand RNA
Minus strand RNA is the complement to mRNA and must be transcribed to plus-RNA before being translated
-There are double stranded RNA viruses and double stranded DNA viruses
Viroids
Small rings of naked RNA without capsids; only infect plants
Prions
Reproduce without DNA or RNA
Defenses against Viral Infection
- Humans fight viral infections with antibodies that bind to the protein and with cytotoxic T cells which destroy infected cells
- Although the envelope is borrowed from the host cell spike proteins encoded from viral nucleic acids protrude from the envelope.
- These proteins bind to receptors on a new host cell causing the virus to be infectious
- Spike proteins allow human antibodies to recognize them when fighting infection
- Since RNA polymerase has no proofreading mechanism the spike proteins change
- Vaccine-injection of antibodies or an injection of a nonpathogenic virus with the same capsid or envelope
- The latter allows the immune system to make its own antibodies
Carrier Population
Even if all viral infections of a certain type were eliminated in humans the virus could still live in another animal until it mutates again
Prokaryotes
- Do not have a membrane bound nucleus
- instead of a nucleus they have a single, circular double stranded DNA molecule that is twisted into supercoils and associated with histones in Archaea and other proteins in bacteria.
- Have a nucleoid
- Have no complex, membrane-bound organelles
- Split into two domains: Archaea and Bacteria
Found in salty lakes and boiling hot springs
-Cell walls of Archaea are not made from peptidoglycan
Nucleoid
The RNA and protein complex in prokaryotes; called the chromatin body, nuclear region, or nuclear body
-Not enclosed by a membrane
Autotrophs
organisms that are capable of using CO2 as their sole source of carbon
Heterotrophs
Use preformed, organic molecules as source of carbon. This carbon comes from other organisms-living or dead
All organisms acquire energy from one of two sources
light
oxidation of organic or inorganic matter
Phototrophs
organisms that use light as their energy source
Chemotrophs
Those that use oxidation of organic or inorganic matter
Nitrogen Fixation
- Some bacteria are capable of fixing nitrogen
- Process by which N2 is converted to ammonia
- Most plants can’t use ammonia and wait for bacteria to process it through nitrification
Nitrification
- Two step process that creates nitrates
- Requires two genera of chemoautotrophic prokaryotes
- NH4^+. + 1.5 O2 —–>NO2^- + H2O+2H^+
NO2^- +. 0.5 O2—–> NO3^-
Chemoautotrophy
Is an inefficient mechanism for acquiring energy so chemoautotrophs require large amounts of substrate
Two Shapes of bacteria
Cocci-round
bacilli-rod shaped
Helically shaped bacteria are called spirilla if they are rigid or otherwise are called spirochetes
Mesosome
Invaginations of the plasma membrane
Plasma Membrane
Phospholipid bilayer that surrounds the cytosol
Phospholipid: Composed of phosphate group, two fatty acid chains, and a glcyerol backbone
Micelle
Spherical structure that’s formed when amphipathic proteins are placed in a liquid… hydrophobic parts inside
-Unlike eukaryotic membranes, prokaryotic plasma membranes don’t contain
Steroids such as cholesterol
Membrane proteins act as
transporters, receptors, attachment sites, and enzymes
Integral/intrinsic protein
Amphipathic proteins that transverse the membrane from the inside to out the outside
Peripheral/extrinsic proteins
situated entirely on surface of the membrane
- ionically bonded to integral proteins or the polar group of a lipid
- Both integral and peripheral proteins can contain carbohydrate chains making them glycoproteins
Carbohydrate portion obviously always protrudes
Lipoproteins
Lipid anchored proteins exist in some plasma membranes with the lipid portions embedded in the membrane and protein portions at the surfaces
Fluid Mosaic Model
Membranes are fluid; parts can move laterally but it can’t separate
-In eukaryotes cholesterol moderates membrane fluidity
Membrane
Not only a barrier but actually creates the different compositions
Electrical Gradient
Points in the direction a positively charged particle will tend to move
+—> -
Semi-permeability
What you call a membrane that slows diffusion
- two factors that affect it: size and polarity
- Larger the molecule the less permeable the membrane is and the more polar the particle the less permeable
Facilitated Diffusion
When transport or carrier proteins help highly charged or large size molecules across the membrane
-Makes the membrane selectively permeable
Active Transport
Movement of a compound against its electrochemical gradient
-Uses energy; either ATP directly or can use ATP to create an electrochemical gradient and then using the energy of the gradient to acquire or expel a molecule… this is secondary active transport
Bacterial Envelope
Surrounds the protoplast—the bacterial plasma membrane and everything inside of it.
Most bacteria are hypertonic to their environment meaning the aqueous solution inside contains more particles
When hydrostatic pressure equals osmotic pressure (remember, this is a pulling force of water to concentrated solute areas) the filling of the cell stops; the strong cell wall protects from rupture
Peptidoglycan
Cell wall is made of it; it’s porous
- Series of disaccharide polymer chains with amino acids
- Lysosome attacks the linkage in humans causing the cell to lyse
Gram Staining
Gram-Positive: Shows up purple; thick peptidoglycan cell wall prevents the gram stain from leaking out
-Periplasmic space is area between cell wall and internal membrane
Gram negative-Shows up pink; outside the cell wall gram negative bacteria have a phospholipid bilayer
This second membrane is more permeable than the first and resembles the plasma membrane.Gram - are harder to kill.
Lipopolysaccharides
The polysaccharide is along chain of carbohydrate which protrudes outward from the cell and can form a protective barrier from antibiotics and antibodies.
The periplasmic space in gram negative bacteria is between this membrane and the cell wall
Capsule or slime layer
Capsules protect bacterium from phagocytosis, dessication, some viruses, and immune responses of host
Bacterial Flagellum
- Made of long, hollow, rigid, helical cylinders made from a globular protein called flagellin
- Rotate counterclockwise to move the bacteria in a single direction
- When they rotate counterclockwise the bacteria tumbles and changes direction
- NOT to be confused with eukaryotic flagella which are made out of microtubules
- Flagellum propelled using energy from a proton gradient rather than by ATP
Binary Fission
A type of asexual reproduction
- Circular DNA is replicated
- Two DNA polymerases begin at the same point (origin of replication) and move in opposite directions making complementary single strands that combine with their template strand to form two complete DNA double stranded circles.
- Then the cell divides leaving one circular chromosome in each daughter cell
- The two daughter cells are genetically identical.
Conjugation
-Requires that one bacterium have a plasmid that codes for a sex pilus
Plasmid
Small circle of DNA that exist and replicate independently of the bacterial chromosome
- Not essential to the bacteria that carry them
- If the plasmid can integrate into the chromosome its called an episome
Sex Pilus
Hollow protein tube that connects two bacterium allowing for DNA transfer
- Passage of DNA is ALWAYS from cell containing the conjugating plasmid to the cell that doesn’t
- The plasmid replicates differently than the circular chromosome
- One strand is nicked, and one end of this strand begins to separate from its complement as its replacement is replicated
- The loose strand is then replicated and fed through the pilus
F plasmid
Fertility factor, a plasmid with the F factor is F+
-If in the form of an episode and if the plus is made while the F factor is integrated into the chromosome some or all of the rest of the chromosome may be replicated and transferred
R plasmid
Donates resistance to antibodies
Transformation
The process by which bacteria may incorporate DNA from their external environment into their genome
Transduction
- Sometimes the capsid of a bacteriophage will mistakenly encapsulate a DNA fragment of the host cell. When these virions infect a new bacterium they inject harmless bacterial DNA fragments instead of virulent viral DNA fragments.
- The virus that mediates transduction is called the vector
Endospores
Some gram positive material form spores that can lie dormant for hundreds of years
- Resistance to heat, UV, dessication, chemical agents
- Formation is usually triggered by a lack of nutrients
In endospore formation the bacterium divides within its own cell wall, then one side engulfs the other
- The cell wall of the engulfed bacterium changes slightly to form the cortex of the endospore
- Several protein layers lie over the cortex to form the resistant structure called the spore coat
- The outer cell then lyses releasing the dormant endospore
- The endospore must be activated before it can germinate and grow
- Activation involves heating, germination is triggered by nutrients
Fungi
Separated into divisions, not phyla
All are eukaryotic heterotrophs that obtain their food by absorption instead of digestion
-Secrete digestive enzymes outside their bodies and then absorb the products
Saprophytic
Feed on the dead- most fungi
-Although some aren’t and they are potent pathogens
Septa
Cell walls made of a polysaccharide chitin
- Perforated to allow exchange to cytoplasm between cells, called cytoplasmic streaming
- Cytoplasmic streaming-allows for rapid growth
Chitin
More resistant to microbial attack than cellulose
Fungi Traits
Spend most of their lives in a haploid state
- with the exception of yeast they are multicellular
- lack centrioles
mitosis takes places only in the nucleus
cells can contain many nuclei which many not be identical
Mycelium
In their growth state they exist as a tangled mass of hyphae
Hyphae
Multiple thread like structures
Can form reproductive structures that give off haploid spores that give rise to new mycelia through asexual reproduction
Fungal Reproduction
Fungi alternate between haploid and diploid but are mostly diploid
- Hyphae are haploid
- Yeast-don’t give off spores; reproduce by budding
Budding (cell fission)-smaller cell pinches off from the single parent
- When sexual reproduction occurs it is between mycelia from two different mating types, + and -
- Forms a diploid zygospore that then undergoes meiosis to form haploid mycelium colony
When do sexual and asexual reproduction occur?
Asexual repro normally happens when conditions are good, so that the offspring has a good chance of surviving
Sexual repro normally occurs when conditions are tough; the hope is that mutations might make the offspring more fit for the environment
