Bio Exam 2
Cell & Structures
Ability of a cell -
can self replicate
has a complex internal structure
has their own metabolism to carry out life functions such as respiration
Ability of a Virus -
viruses can infect host cells and hijack their machinery to reproduce, although they lack the cellular structures necessary for independent life.
Characteristics of Light microscope -
Uses visible light to magnify specimens, allowing for the observation of cellular structures and microorganisms. Light microscopes have limitations in resolution, making them less effective for viewing smaller viruses compared to electron microscopes, which utilize electron beams for higher magnification.
Characteristics of SEM microscope -
Scanning Electron Microscope (SEM) uses a focused beam of electrons to scan the surface of a specimen, providing detailed three-dimensional images at high magnification.
SEM has a much higher resolution than light microscopes, making it suitable for observing the fine details of viruses and other nanostructures.
It requires specimens to be coated with a conductive material, which can alter the natural state of biological samples.
Characteristics of TEM microscope -
Transmission Electron Microscope (TEM) transmits electrons through a thin specimen, providing two-dimensional images with even higher resolution than SEM.
TEM is ideal for examining the internal structure of cells and tissues at the atomic level.
Unlike SEM, TEM requires samples to be extremely thin, typically less than 100 nanometers, to allow electron penetration.
Magnification Definition -
Using the lenses on a microscope to zoom into or out of a specimen
Resolution Definition -
Using the lenses on a microscope to make a two images of a specimen one clear image
Robert Hooke’s contribution to cell biology -
introduced the term "cell" after observing cork and plant tissues under a microscope, laying the foundation for cell theory.
Cell theory - A fundamental concept in biology that states:
All living organisms are composed of one or more cells.
The cell is the basic unit of life.
All cells arise from pre-existing cells.
Developed the first microscope
Cytology -
The study of cells and their physiological structures
Biochemistry -
The branch of science that explores the chemical processes and substances that occur within living organisms.
Cell Fractionation -
A technique used to separate cellular components while preserving their individual functions, allowing researchers to study specific organelles and their roles in cellular processes.
Process: Cells are broken down into a mixture using a blender through Homogenization, Centrifugation - pinning the cell mixture at different speeds to separate components based on its density and size, placed in Isotonic solution to prevent damage to the organelles, product is used to study specific organelles within a cell
Size limitations of cells -
Cells are small due to the limitations imposed by their surface area to volume ratio, as a cell gets larger its volume increases much faster than its surface area, making it difficult to efficiently transport nutrients in and waste products out through the cell membrane.
Smaller cells have a greater surface area relative to their volume allowing for more efficient transport and better functioning.
Similarities in structures for Prokaryotic and Eukaryotic cells
Has a cell membrane, contains DNA, ribosomes, and has the ability to divide and reproduce.
Differences in structures for Prokaryotic and Eukaryotic cells
Prokaryotic lacks a nucleus and other membrane-bound organelles
Eukaryotic has a nucleus and various organelles within its cytoplasm
(eye resolution-100nm)
Structures of a cell and their uses
Nucleus: Chromatin, Nucleolus - Only Eukaryotic
Endoplasmic Reticulum: Rough ER, Smooth ER -
Flagellum - all cells
Centrosome - animal cells / most eukaryotic cells
Peroxisome - almost all eukaryotic cells
Microvilli - eukaryotic animal cells
Cytoskeleton - all eukaryotic cells
Lysosome -
Mitochondria
Plasma Membrane
Golgi Apparatus
Ribosomes
Structures found in all cells: DNA, Plasma Membrane, Ribosomes(makes proteins), Cytosol/Cytoplasm (fluid inside the cell)
Structures found in eukaryotic cells: Nucleus, nucleolus (in charge of making ribosmomes), endoplasmic reticulum (rough-ribosomes (proteins) and smooth-no proteins), Cytoskeleton (), centrosome (where all the proteins radiate), mitochondria (powerhouse of the cell/atp factory), vacuole, chloroplasts, lysosomes, golgi apparatus
Animal cells: Flagellum, Centrioles, Lysosomes(a container filled with digestion enzymes), Microvilli (finger-like projections), cilia
Plant cells: Cell Wall, Plasmodesmata, Chloroplast(used in photosynthesis), Central Vacuole(containers/stores) Tonoplast (plast=plant structure), nucleus, endoplasmic reticulum, golgi apparatus, ribosomes, mitochondria, plastids and a cell membrane
Structures found in prokaryotic cells : Nucleoid, Pili, Peptidoglycan(protein/sugar), Capsule, ribosomes, cell membrane and cell wall
Structures found in plants not animals: Chloroplasts, cell walls, and a large central vacuole
Where to find the:
nucleus - purple ball
nucleoid - prokaryote
chromatin - surrounded by the nucleolus like little hairs
plasma membrane - lining of the cell in both animal and plant cells
cell wall - only found in plants
microvilli - on animal cells
Integrin - tombstones nestled in between plasma membrane
Desosomes - between cells to provide strong adhesion, have little hairs
Tight Junctions - found on plasma membrane, used to create an airtight seal between cells
Gap junction - on outer part of cell, used to communicate with other cells
Cellular Respiration
Anabolism - stores energy (synthesis reactions)
Catabolism - releases energy (degradation reactions)
Autotrophs (self-feeder): Producers (plants, algae, bacteria)
Heterotrophs: Consumers (animals,bugs, humans, some bacteria)
Catabolism types:
Respiration (complete breakdown of sugar) (Sugar + O2 → H20 + CO2)
Aerobic (requires O2)
How many respirations are made from a single glucose molecule? - 30-32 ATP
Anaerobic (works without O2) - >2 +<30 ATP (less efficient compared to respiration)
Fermentation (incomplete breakdown of sugar)
The process where organisms generate energy by breaking down glucose without oxygen
Steps: (1) Glycolysis: breaks down glucose into pyruvate
(2) Lactic Acid - Pyruvate accepts electrons from NADH and converts to lactic acid and regenerates NAD+ which is needed to repeat the cycle
(2) Ethanol: Pyruvate is decarboxylated to release CO2 and forms acetaldenyde which is reduced by NADH and produces ethanol , then regenerates NAD+ to repeat cycle
The process of fermentation is similar to respiration because both are processes to generate energy from glucose
It is different because fermentation occurs without oxygen (anaerobic) while cellular respiration requires oxygen (aerobic) - through this, fermentation creates less ATP than that of respiration making it less efficient - This happens to us when we undergo strenuous exercise
ATP (Adenosine Triphosphate) and ADP (Adenosine Diphosphate) are energy-carrying molecules found in all living cells, where ATP acts as the primary "energy currency" by releasing energy when it converts to ADP by losing a phosphate group
NADH (Nicotinamide Adenine Dinucleotide - reduced form) and NAD+ (oxidized form) and FADH2 (Flavin Adenine Dinucleotide - reduced form) and FAD (oxidized form) are coenzymes involved in cellular respiration, primarily found in the mitochondria, that carry electrons and hydrogen ions to the electron transport chain to generate ATP
ATP Synthase is the enzyme that makes ATP (the molecular “mill”)
NADH and FADH are the two elements that power the production of ATP
Redox reaction - loss of equally sharing electrons/movement of electrons
Oxidation - adding an electron
Electron carrier/acceptors: NADH & FADH2 as electron (energy) shuttles
Glycolysis happens in the Cytosol/Cytoplasm
Krebs Cycle happens in the Mitochondrial Matrix
Electron Transport happens in the Inner membrane/Cristae
Glycolysis Celular respiration steps:
2 ATP and 2 NADH2s
Int. Step 2 NADH
Krebs Cycle steps:
2 ATP
6 NADH
2 FADH2s
Electron Transport - 26-28 ATP
Following the Carbon - 6 carbons in, 6 CO2s out
Glycolysis details:
Invest: 2 ATP
Energy Payoff: 4 ATP
Enzyme that causes each reaction in glycolysis
Each ADH is 2 ½ atp
Fadh is 1 ½ atp
Electron Transport Chain:
like a conveyor belt, transporting protein down the line (losing energy while going down the line/every oval)
a series of protein complexes embedded in a membrane that transfer electrons from donor molecules to oxygen, generating a proton gradient which is then used to produce ATP through ATP synthase
In bacteria the krebs cycle and the glycolysis cycle happens in the cytoplasm/cytosol while our cells differ
Catabolism of Fats and Proteins
Fats and proteins cannot directly enter the respiratory pathway; they must first be broken down into smaller molecules - fatty acids and glycerol for fats, and amino acids for proteins - which then can be converted into intermediates that can join the pathway, typically entering at the level of acetyl-CoA in the Krebs cycle
Compare and contrast Respiration as it occurs in Bacteria - Bacteria lack intracellular compartments, called organelles, that other cells have. Thus, in bacteria cellular respiration takes place in the cytoplasm and at the plasma membrane
Photosynthesis:
2 types of autotrophs:
-Photoautotrophs (and)- plants, algae, some protists, some prokaryotes - uses light to make food
Plant needs to make sugars: nitrogen, phosphate and potassium
Chemoautotrophs - uses chemicals from hydrothermal vents as well as tube worms (won’t be covered any further) (majority of oxygen comes from water).
Nature of light
Light - source if chemical energy on earth - what powers photosynthesis - combinations of different wavelengths/what determines color for us - longest: red, shortest: purple - shorter waves=more energy
“Producers”: uses light, water and carbon dioxide to create sugar : NPK
Infrared: Invisible to the human eye but can be felt if walked near (hot stove)
Gamma rays - longest wavelength - red
x-rays - medical imaging - purple blue
ultra-violet - causes sunburn - UV
visible light - what we can see - what our eyes interpret as color
Infrared radiation - emitted by heat source - yellow
microwaves - used in microwave ovens -orange
Radio waves - longest wave - red - used in radio communications
absorption - process of a pigment within the leaf taking in specific wavelengths of light
reflection - refers to the light that bounces back from the leaf surface
transmission - the light that passes through the leaf
the color we see from a leaf is determined by the wavelengths of light it primarily reflects
Chlorophyll a - found in all plants and algae - absorbs light energy for photosynthesis
chlorophyll b - found in most plants and green algae, helps absorb broader range of wavelengths
chlorophyll c - found in marine algae like diatoms and brown algae
a,b, and ca are embedded within the thylakoid membranes of chloroplasts
The pigments absorb light energy from the sun and then transfer that energy to a reaction center where it can be converted into chemical energy
Steps:
light absorption, Excited energy is then passed from pne pigment molecule to another within the antenna complex moving toward reaction center, once at reaction center the excited electron is transferred to an electron acceptor molecule, initiating a chain of electron transfer reactions that produce ATP and NADPH
Chloroplasts structure and functions:
outer, intermediate and inner membrane
Stroma - site of the calvin cycle - looks like connections between thylakoids
thylakoids - where light energy is converted to ATP and NADPH - little tablets
grana - increases the efficiency of light capture by stacking thylakoids together - basically stacked thylakoids, where photosynthesis occurs
Photosynthesis Equation: (carbon dioxide to come in)CO2+H2O-> Sugar+O2(oxygen to come out) - opposite of respiration
Light Trapping Pigments:
Chlorophylls: CH A(Blue/green algae and all eukaryotes), CH B(green algae and plants), CH C (Diatoms, Brown Algae)
Others: Carotenoids, Phycocyanins, Anthocyanins, etc.
Layers of the leaf:
Epidermis - surface
Mesophyll area (where photosynthesis happens) (sandwiched in between) (inside the cell)
Stomata (holes for air to get in and out of the cell)
Gran is where photosynthesis occurs
Stroma is where the liquid is inside of the cell and Thylakoid are the three stacked pancake looking structures inside of the cell
Light reactions and Calvin cycle:
Where do these things happen?
Light reactions = Thylakoid
Calvin Cycle =Stroma (dark reactions)
Light energy powers the calvin cycle with ATP and NADPH (creates energy)
The Calvin cycle (creates sugar):
Rubisco - the enzyme that fixes CO2 into the Calvin cycle
3 CO2 in - power ups 3 times (18 ATP), 3GP falls out at the bottom of the cycle, works its way back up, gains one more G3P(sugar), then is back up at the top of the cycle
-What powers the calvin cycle? ATP and NADPH
Photosystem 11 extracts electrons from water, releasing oxygen
photosystem 1 uses those electrons to generate NADPH which is needed for the Calvin Cycle
What happens to the stomata when it's hot and dry? Stomata deflates and closes.
Lack of CO2 entering the calvin cycle
Build up of O2 (Photorespiration) - cause of death in plants under hot and dry circumstances
C4 plants and CAM plants are able to avoid photorespiration
Anatomy of C4 plant (during the day):
Has a protective layer that can capture rare CO2 and bring it into the Calvin Cycle
Pep Carboxylase - binds the CO2 to the pep and transports and delivers it to calvin cycle - repeat (Taxi Service) (see example on slides)
CAM Plants (Cactus/desert plants) during the night
Close their stomata all day because if they don’t the water in the plant would evaporate
Opens stomata at night to absorb CO2 and release O2 since it’s cold at night (CO2 is part of malic acid)
Photorespiration is a process in plants where the enzyme RuBisCO, which is responsible for carbon fixation during photosynthesis, accidentally binds to oxygen instead of carbon dioxide, leading to the release of carbon dioxide and a loss of fixed carbon, essentially "wasting" energy produced by photosynthesis; this occurs primarily when carbon dioxide levels are low and oxygen levels are high, like in hot, dry conditions where plants may close their stomata to conserve water, limiting CO2 intake.
C4 plants spatially separate the initial carbon fixation from the Calvin cycle within the leaf, while CAM plants separate these processes temporally by fixing carbon dioxide at night and using it during the day; both strategies minimize photorespiration by concentrating CO2 around the enzyme Rubisco.
Cell Division (Mitosis and Cell cycle):
The functions of cell division: Tissue renewal/repair
Growth and Development - egg, embryo, tissue
Eukaryotic Chromosomes - DNA: Copying of DNA is the first step of cell division
DNA division:
-(if stretch out) 3M DNA copied before Mitosis
-New cells receive full Genome
-Cell splits after DNA is allocated
-No dilution
Terminology:
Genome - ones complete set of DNA
Chromosomes - one chromosome =one strand of DNA
Gene - recipe for a protein
Chromatin - the combo of dna and protiens which make chromosomes
Somatic Cells - not a sperm or egg
Germ cell - divide to make the gamet (not a somatic cell)
Gametes - sex cells
Karyotype - a picture of all the chromosomes in a person
Sister Chromatids - identical copies of the same chromosome but still considered as one chromosome since they are connected in the middle
Duplicate Chromosomes - a type of chromosomal mutation called a "duplication" and can occur during cell division when chromosomes are not properly separated
A chromatid is one of the two identical strands that make up a replicated chromosome, essentially acting as a copy of the original chromosome, and their primary function is to ensure accurate distribution of genetic material during cell division by allowing the separation of chromosomes into new daughter cells, each receiving a complete set of DNA
Chromatids are produced during the synthesis (S) phase of interphase when DNA replication occurs
Cell signals, both external and internal, are chemical messengers that cells use to communicate with each other and their environment, triggering specific responses within the cell, such as growth, differentiation, or apoptosis; external signals come from outside the cell and bind to receptors on the cell membrane, while internal signals are generated within the cell itself and can influence various cellular processes
A centromere is a specialized region on a chromosome that acts as the attachment point for spindle fibers during cell division, ensuring that sister chromatids are properly separated and distributed to daughter cells during mitosis and meiosis
Prokaryotic division primarily occurs through a process called binary fission, where a single cell replicates its DNA and divides into two identical daughter cells; however, prokaryotes can also exchange genetic material through horizontal gene transfer mechanisms like transformation, transduction, and conjugation, allowing for genetic diversity beyond simple cell division
Horizontal Gene Transfer Mechanisms:
Transformation:
A prokaryotic cell takes up free DNA fragments from the environment released by other bacteria, incorporating them into its own genome.
Transduction:
A virus (bacteriophage) accidentally transfers DNA from one bacterium to another during its replication cycle.
Conjugation:
Direct transfer of DNA from one bacterium to another through a physical connection called a pilus, where the donor cell transfers genetic material to the recipient cell.
Prokaryotic cell division:
Prokaryotes divide by a simpler process called binary fission, where the single circular chromosome replicates and the cell splits in two, without the need for a mitotic spindle or organized nuclear membrane.
Endosymbiosis theory:
The most widely accepted explanation for the origin of eukaryotes is that they evolved from prokaryotic cells through a process called endosymbiosis, where smaller prokaryotes were engulfed by larger prokaryotes, eventually becoming organelles like mitochondria and chloroplasts.
Development of the nucleus:
A crucial step in the evolution of mitosis was the formation of a nuclear membrane, which allowed for the organization and segregation of linear chromosomes during cell division.
Cytoskeleton involvement:
The evolution of a cytoskeleton within eukaryotes provided the necessary structural support to form the mitotic spindle, a complex apparatus responsible for accurately separating chromosomes during mitosis.
Gradual complexity:
The emergence of mitosis likely involved a gradual increase in complexity, with early eukaryotic ancestors potentially having simpler forms of cell division that gradually evolved into the well-defined stages of mitosis seen in modern eukaryotes.
Different cyclins are expressed at different stages of the cell cycle, such as cyclin D (G1 phase), cyclin E (G1/S transition), cyclin A (S phase), and cyclin B (G2/M transition
Humans have 23 chromosomes - 2 pairs make 46
XY - boy
X - girl
Having an extra chromosome can be fatal or often the cause of down syndrome (Trisomy 13- a third chromosome -fatal )
Monosomy X is the only survivable anomaly
Mitosis - division of the nucleus (eukaryotic cells)
Mitotic Cell Cycle
1. G1 (G0) of interface (growth)
2. (S) DNA synthesis - making copies of DNA
3. G2 interface (growth)
Cycle continues…
(interface looks like a clean circular nuclei with dark patches of dots)
4 Phases of Mitosis - happens in the short portion of the mitotic phase
Prophase - chromosomes cluster up, spindle fibers start to form
Metaphase - chromosomes are lined up within the spindles
Anaphase - chromatids are yanked apart and migrate to opposite ends of the cell
Telophase - two cells start to form around the two clusters of chromosomes, they start to form into a new nucleus
Telophase and cytokinesis happen at the same time
In a plant cell a wall is built in between the two nuclei that were just formed.
Cyclin Dependent Kinase (CDK) inactivated - checkpoints on the cell division dial (type of enzyme) (G1, G2, M)
Key characteristics of DNA structure:
Double Helix:
The two strands of DNA twist around each other to form a helical shape, resembling a twisted ladder.
Base Pairing:
Specific base pairs always form between the strands: Adenine (A) pairs with Thymine (T) and Cytosine (C) pairs with Guanine (G).
Hydrogen Bonds:
The base pairs are held together by weak hydrogen bonds.
Antiparallel Strands:
The two strands run in opposite directions, meaning one strand has a 5' end (phosphate group) at one end and a 3' end (hydroxyl group) at the other, and the complementary strand has the opposite arrangement.
Nucleotide Structure:
Each "rung" of the DNA ladder is made up of a nucleotide, which consists of a sugar molecule (deoxyribose), a phosphate group, and a nitrogenous base.
Genetic Code:
The sequence of bases along the DNA molecule determines the genetic code, which instructs the cell on how to build proteins.
Internal signals that control the cycle:
Mitotic prophase factor, anaphase promoting complex
External signals: growth factors
Platelet derived growth factor
Prokaryotic cell division: Binary fision - grows, copies dna and divides in two cells
Every gene is on the locus part of the chromosome
Aesexual Reproductiom - clones off of itself
Sexual Reproduction involves haploid gamets (one half from mom and one from dad) and form diploit zygotes (both sides together)
Sex chromosome - x+y
Autosome - everything but the sex chromosomes
Homologous Pairs - one signle pair of chromosomes
During early prophase the chromosomes bundle up on top of each other and exchange parts of themselves in the process of Chiasmata and in turn create new genes
The arrangement of chromosomes producing gametes are completely random therefore there there are many different arrangements that can be made
Prokaryotic cell: genetic change (Prok.s clones its dna)-
Mutations are the source of mistakes in dna
Transformation - alive cell picks up dna from a bacterial cell land incorporate it into itself
Transduction - virus injects dna into cell and the cell becomes a factory for making new viruses
Conjugation - two bacterial cells exchange dna
–Genetics
Characters - Heritable feature ex. Flower color, eye color etc.
Trait - Variant of a character (controlled by distinct copies of genes) (Alleles = alternate version of the same genes) ex. Pink petals, blue eyes, six fingers
The father of modern genetics - Gregor Mendel - experiments on peas - Studied recessive and dominant traits - tracked heritable characters for three generations through the process of test crossing
incomplete dominance- red and white make pink
co-dominance - two dominant
x-linked - the gene causing the trait or the disorder is located on the X chromosome
pleiotrophy - a type of genetic expression in which only one gene affects multiple traits (sickle cell)
epistasis - a genetic phenomenon where the expression of one gene is influenced by the expression of one or more other genes (rats)
polygenic inheritance - a pattern of genetic inheritance where multiple genes control a trait or characteristic
environmental impact - refers to how external factors like diet, temperature, sunlight, toxins, and social conditions can influence the development and expression of an organism's characteristics
multifactoral - characteristics or diseases that are influenced by a combination of genetic and environmental factors
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