Biology All-in-one Flashcards
Vasopressin
GFR (Glomular Filtration Rate)
사구체 여과율
The amount of blood filtered / Minute
- 90~120mL/min
Axon Hillock (축삭둔덕)
A cone-shaped region of a neuron’s cell body that serves as the origin of the axon
Anisogamy (이형접합)
Sexual Reproduction involving fusion of two gametes differing in size
Genomic Imprinting (유전체 각인)
Epigenetic phenomenon
Some genes being expressed from one parent’s chromosome
Biosphere / ecosphere
생물권
Worldwide sum of all ecosystems
Biome (군계)
A distinct geographical region with specific climate, vegetation, and animal life.
Community (군집)
A group or association of populations of two or more different species occupying the same geographical area at the same time.
Population (개체군)
a group of organisms of the same species that live in the same area and can breed with each other
Organism (개체)
An organism is any living thing that functions as an individual
Organ (system)
기관 (계)
A collection of tissues joined in a structural unit to serve a common function
Tissue
조직
An assembly of similar cells and their extracellular matrix from the same embryonic origin that together carry out a specific function.
4 Types of tissue
Epithelial Tissue (상피조직)
Connective Tissue (결합조직)
Muscle Tissue (근육조직)
Nervous Tissue (신경조직)
Viroid
Small single-stranded, circular RNAs that are infectious pathogens.
Domain (영역)
Archaea (고세균)
Eubacteria (진정세균)
Eukaryota (진핵생물)
Kingdom (계)
Animalia (동물계)
Plantae (식물계)
Fungi (균계)
Protista (원생생물계)
Archaea (고세균계)
Eubacteria (진정세균계)
Used to have monera instead of Archaea and Bacteria
Archaea (고세균계) - examples
Methanogen (메테인 세균)
Hyperthermophiles (극호열성균)
Hyperhalophiles (극호염성 세균)
Why was Monera separated into Archaea and Eubacteria
rRNA difference
6 Most abundant element in human by mass
O (65%)
C (18.5%)
H (9.5%)
N (3.3%)
Ca (1.5%)
P (1.0%)
6 Most abundant element in plant by mass
C, O, H, N, K, Ca, Mg, P, S
Types of Radioactive Isotopes (H, P, S, C, I)
H3
P32
S35
C14
I125
Draw ribose
Draw deoxyribose
Kinase vs phosphorylase
Kinase (인산화 효소) - addition of PO4 from ATP or GTP -> no covalent bond broken
Phosphorylase (가인산분해효소) - Addition of inorganic PO4 -> breaks bond in substrate
Kinase vs Phosphatase
Kinase (인산화 효소) adds
Phosphatase (탈인산화효소) removes
Radioactive isotopes in:
Gamma position vs
Alpha position
Alpha - Used as ATP/dATP itself -> DNA/RNA synthesis
Gamma -> used in phosphorylation
Radioactive sulfur is used in what AAs
Cystein
Methionine
Covalent bond electronegativity difference
<1.7
Polar / non-polar covalent electronegativity difference
<1.4 non
>1.4 polar
Functional Groups
- Carboxyl
R-COOH
exists as R-COO(-) in water
Functional Groups
- Hydroxyl
R-OH
Functional Groups
- Carbonyl
R-(C=O)-R’
Ketone if in middle
Aldehyde if at end
Functional Groups
- Amine (아미노기)
-NH2
exists as -NH3+ in water
Functional Groups
- Sulfide / Thiol
R-S-R’ / R-SH
책에는 설파이드 R-SH로 나와있음
used in disulfide bridge
Functional Groups
- Phosphate (인산기)
R-OPO3 (2-)
Isomer
Molecules or polyatomic ions with identical molecular formula.
Structural Isomers
Constitutional Isomers
구조이성질체
Molecules that have the same chemical formula but different arrangements of atoms and bonds
Stereoisomers
입체이성질체
Differ only in the spatial orientation of the groups
Chiral Carbon
비대칭 탄소
Carbon bonded to 4 different organic groups
D/L isomer determination
Larger group (usually NH3 or OH) on the bottom most carbon in fischer projection
Are natural AAs D or L form
L form
Are natural sugars D or L form
D form
Draw in fischer form
Alpha-D-Glucose
vs
Beta-D-Glucose
Draw in chair form
Alpha-D-Glucose
vs
Beta-D-Glucose
Diastereomer
부분입체이성질체
Stereoisomers that are non-identical, non-superimposable, and do not have mirror images
Enantiomer (거울 이성질체)
Molecules that are mirror images of one another but cannot be superimposed one upon the other
S-R configuration
Priority spinning Right (Rectus)
vs
Priority spining Left (Sinister)
Ibuprofen effective form
S form
R no effect
Albuterol effective form
R form
S inhibits effect
Differential centrifugation
편차 원심분리 / 차동원심분리
Using increasing G force to separate substances
Cellular Fractionation
세포 분획
1,000G 10min - Cells / Nucleus
20,000G 20min - Mitocondria, Lysosome, Peroxisome
100,000G 1hr - Smaller Cellular Substances (Microsomes)
200,000G 3hrs - Ribosome
Nucleus - chloroplast - mitocondria for plants
Emergent Properties (창발적 특성) of H2O
Polar -> Good Solvent - most biological substrates are polar
H-bond
- Strong connection - surface tension
- High boiling point / heat capacity
- Higher density at 4.C
DNA charge at pH 7.2
(-)
Nucleoside vs Nucleotide
Nucleoside + (PO4)n = Nucleotide
Four Bases
R: Adenine Cytosine
Y: Thymine Guanine
Pyrophosphate
(PO4)2
Why is it important to not use U in DNA?
Why is T used instead of U?
Deamination of C will result in U. It’s confusing.
Draw DNA/RNA bases
Draw Ribose and Deoxyribose
Deamination of Adenine forms…
inosine
Characteristics of DNA
- Double Stranded
- Antiparallel
- Complementarity
- Double helix
- Major groove / minor groove
Why does DNA appear negatively charged
Bases -> non-polar
PO4/d-ribose -> polar
Outside is PO3- => loses H+ in pH 7.2
TF binds to DNA in major or minor groove
Major
Exception: TATAbox BP
Three forms of DNA and where it’s observed.
A: Humidity <75% / DNA-RNA / RNA-RNA
B: Normal
Z(left handed): GC repeat / High-salt env
DNA Tm per base type
A-T: ~2˚C
G-C: ~3-4˚C
B-form DNA numbers
Width 2nm
Distance between adj nucleotide: 0.34nm
One turn: 10bp 3.4nm
Width 2.3nm
One turn: 11bp 2.86nm
Chargaff”s rule
A:G=T:C
If A=30%, T=15% what is happening according to Chargaff’s rule
It’s single strand or damaged
Normality
Basically number of charge it releases.
1M HCl -> 1N HCl
1M CaCl2 -> 2N Ca2+ / 2N Cl
Denaturation of DNA
Tm
Alkaline solution: 0.2N NaOH
Adding acid to DNA
Depurination
Fragmentation of DNA
PCR Process
Central Dogma
DNA -> RNA -> Protein
Template/non-template strand Elaborate every detail
Template = antisense = non-coding = (-)strand
Non-template = sense = coding = (+)strand
Codons on sense read in 5’->3’
Template is used 3’->5’ to build sense 5’->3’
20 Amino Acids
AAs with non-polar R
G, A, V, L, I, M, F, W, P
AAs with uncharged polar R
C, S, T, Y, N, Q
Acidic AA
D, E
Basic AA
H, K, R
Essential Amino acids
I, L, V, F, W, H, K, T, M
Henderson Hasselbalch equation
pI
Isoelectric point
charge-neutral point
What acts as Peptidyl Transferase?
rRNA
- 23S in Prokaryotes
- 28S in Eukaryotes
Characteristics of a peptide bond
- Resonance between OCN
- Forms a plane-like structure
- Restricts rotation
Three main (+1) secondary protein structure
Alpha helices
Beta pleated sheet
Beta turns
+ Omega Loops
Alpha helices
Tight right-handed coils
3.6 AA per turn
Beta pleated sheets
Polypeptide chains lying side by side
Connected with hydrogen bonds
Is Protein folding reversible or irreversible? and Why?
Reversible
All the bonds in secondary~quaternary structure are weak bonds.
Sequence remains while folding changes
Chaperonin
Oligomers
Provide favorable conditions for the correct folding of proteins.
GroEL/GroES and TRiC
Chaperones
Mostly HSPs
Monomers
Assists folding by attaching
What bond forms secondary structure of protein
H-bonds between peptide bonds
Order of forming tertiary structure of protein
- Nonpolar Rs
- H-bonds / Ioninc bonds
- Disulfide bridges
What AA forms disulfide bridges. (3 letter code + 1 letter code)
Cys / C
What is a co-factor?
A non-protein chemical compound or metallic ion that is required for an enzyme’s role as a catalyst
Protein Denaturation
A process that alters a protein’s structure, making it unable to perform its function.
Basically from tertiary(Quaternary) to primary structure
Causes of protein denaturation
Temperature
Surfactant - SDS
Reducing Agents - B-mercaptoethanol / DTT
Organic Solvents - Phenol / Chloroform / Ether
pH change - Changes the ionic bonds within the protein
Salt concentration - Alters bonds
SDS-PAGE
Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis
Reducing agent used for protein denaturation
Beta-mercaptoethanol
- Reduce disulfide bonds
DTT (Dithiothreitol)
Crosslinking
Formaldehyde
- Forms covalent bonds where it shouldn’t in protein
- Technically not denaturation
Electrophoresis separates by what
Size and Charge
- Only size for DNA/RNA
Types of Gel and their use
Agarose
- DNA / RNA
- Protein (for charge separation)
SDS PAGE
- Protein (size separation)
PAGE
- Protein (charge separation)
EtBr
Ethidium Bromide
- Fluorescence for DNA/RNA
Dye for Protein in Agarose
Coomassie Blue
Describe the process for SDS PAGE
DISC (Discontinuous Gel)
SDS + Beta- mercaptoethanol + PA gel
- Stacking gel - 3-5% / pH6.8
- Resolving gel - 6-15% / pH8.8
Vertical Separation
In Stacking gel - Gly, Protein, Cl-
In Resolving gel - Protein, Gly, Cl-
DISC gel
Discontinuous gel
- Discontinuous in pH and Conc.
2-D Gel Electrophoresis
Separates protein by pI
- Agarose or Polyampholyte PAGE
Then do SDS-PAGE (Size)
Agarose Electrophoresis vs Polyampholyte PAGE
Agarose (pH7.0) separates y pI but it doesn’t stop
Polyampholyte has a pH gradient so the protein stops at its pI
Pleiotropy
a genetic phenomenon where a single gene or DNA variant influences multiple traits or phenotypic characteristics
유사분열 / 무사분열
With spindle / without spindle
분배계수가 높으면 투과성이 좋다/나쁘다
좋다
Properties of Phospholipid
- Semi-permeability
- Fluidity
What affects membrane’s fluidity
High T -> more fluid
Unsaturated lipid -> more fluid
What bond is formed between the head and tail
Ester bond
Types of phospholipid in the plasma membrane
Outer Membrane:
- Phosphatidylcholine (PC)
Inner Membrane:
- Phosphatidylethanolamine (PE)
- Phosphatidylserine (PS)
- Phosphatidylinositol (PI)
What is flippase?
- ATP-powered pumps that belong to the P4-ATPase family
- Moves lipids from the extracellular layer to the cytosolic layer.
What is floppase?
- ATP-binding cassette (ABC) transporters.
- Moves lipids from the cytosolic layer to the extracellular layer.
What are Scramblases?
Proteins that move phospholipids between the two layers of a cell membrane’s lipid bilayer.
- A part of Flippase family
Role of Scramblases
- Viral infection:
- Involved in SARS-CoV-2 pathogenesis - Apoptosis
- Activated in response to apoptotic signals. - Blood Coagulation
- Activated in response to blood coagulation signals. - Autophagy
- Cell-cell infusion
What types of lipids are abundant in the outer leaflet of plasma membrane?
- PC / Phosphatidylcholine
- SM / Sphingomyelin
Categories of membrane protein based on its position
Integral
Transmembrane
Peripheral
Characteristics of membrane protein.
- AAs with non-polar R group in the inside the membrane
Tyrosine’s position in a phospholipid layer
Between the lipid and ECM or Lipid and cytosol
- Due to its hydroxyl(polar) and phenyl (non-polar) group
Role of Cholesterol in membrane
Controls the fluidity
- Low temp -> separates the phospholipids
- High temp -> physically restricts movement
Forms of carbohydrates in membrane
- Glycoprotein
- Glycosphingolipids (GSL) or other glycolipids
Both only on the outer leaflet
How is glycoprotein formed
- Dolicol contains carb inside the lumen of ER
- Carb transferred onto the protein’s ASN (N) (Glycosylation)
What is FRET and how is it used
FRET: Fluorescence Resonance Energy Transfer
1. Fluorescence-tagged protein A-B
2. Certain frequency light provided
3. If A, B are close/bound together, FRET occurs to change light emmited
4. If not original color is shown
What is the use of Triton X-100
A non-ionic surfactant used to separate membranes.
What is a lipid raft and what are its characteristics?
A “raft” of membrane tied together - isn’t separated by triton X-100
High in:
- Cholesterol
- Glycoprotein
- Long FA chain lipids
- Saturated FA
Partition Coefficient (분배계수) formula
P = [Substrate in Hydrophobic Solvent] / [Substrate in Hydrophilic Solvent]
Substrates that are highly permeable through plasma membrane
Substrates of high partition coefficient
- Steroids
- Gas
- FA < 12 Cs
- Water* is hydrophilic but ALMOST all cells (except loop of Henle and collective tube) have aquaporins
Michaelis-Menten equation
Used to measure the reaction rate of enzyme reactions.
V0 = Vmax * [S] / (Km +[S])
V0 = Kcat * [E] * [S] / (Km +[S])
V0 = reaction rate
Vmax = limiting rate (at saturation)
Km = michaelis constant - [S] at 1/2Vmax
Use Kt instead of Km for carriers but same concept but it’s only notation difference
Equilibrium Potential (평형전위) Equation
R: Universal gas constant - 8.314 J / (K * mol)
T: Temp
z: valence of ionic species
F: Faraday’s constant - 96485 C/mol
[]o / []i - [] of in and out ions
Osmotic Pressure Formula
Pi = C * R * T
C = Osmotic molarity (Osm)
R= Gas Constant
T= temp
0.9% NaCl in other units
0.15M or 300mOsm
0.5% Glucose in other units
0.3M / 300mOsm
mOsm of RBC
300mOsm
Is 300mOsm isotonic for RBC?
No.
Glucose will move in to the cell through GLUP forming a hypotonic solution outside
Water potential?
Potential of water molecules to move from a hypotonic solution to a hypertonic solution across a semi-permeable membrane.
자유 물 분자를 가진 정도
Positive W potential means water will leave the environment
Water potential equation
Pressure potential + Solute potential
Types of Passive Transport
- Simple diffusion
- Facilitated diffusion (Channel / Carrier)
Primary and Secondary Active Transport
Primary
- uses energy to form an electrochemical gradient
Secondary
- moves molecules using an electrochemical gradient
Two types of cotransporter based on substrate movement
Symport
- Substrates move in the same direction
Antiport
- Substrates move in the opposite direction
Ionic gradients across plasma membrane
Only the ones higher
Inside:
- K+
Outside
- Na+
- Cl-
- Ca++
Na K Pump action
- 3Na from inside
- ATP
- Na detatch 2K attach
- Back in with 2K + Pi detach
Ca++ Pump distribution
- Pump out of cell
- Pump into ER (Sarcoplasmic Reticulum)
Membrane potential in mV?
inside is -50mV ~ -200mV
Examples of symport and antiport
Symport
1. Na+ - Glucose
Antiport
1. HCO3- - Cl-
2. Na+ - Ca++
What gradient does secondary active transporters use in animals / plants
Animals - Na+
Plants - H+
Explain glucose transport in the SI epithelial cell
- Basal Na-K Pump forms low [Na] in cell
- Apical Na-Glucose cotransporter (symport) brings in glucose through concentration gradient of Na (2Na-1Glucose)
- GLUT2 pumps out glucose into bloodstream
Types of endocytosis (내포작용)
Pinocytosis (음세포 작용)
- “Cell drinking” takes up dissolved nutrients in small vesicles
Phagocytosis (식세포 작용)
- “Cell eating” engulfs large solid molecules / bacteria
- forms pseudopods (위족)
Receptor-mediated Endocytosis
- A process of removing a certain substance from blood/ECM
Cells that perform phagocytosis
- Macrophage (대식세포)
- Dendrites (수지상세포)
- Neutrophils (호중구)
- Eosinophils (호산구)
- B lymphocytes
technically B lymphs can be considered receptor-mediated
Examples of receptor-mediated endocytosis
Removal of LDL
- Detects Apolipoprotein 100 (ApoB100)
Removal of Fe2+
- Detects transferrin
Process of LDL receptor
- LDLR detects ApoB100
- Clathrin coated pit forms
- Dynamin(GTPase) pinches off the vesicle
- Clathrin and LDLR is removed
- Vesicle fuses with lysosome
Coated pit (피막소와)
How does lysosome transport digested molecules into the cytosol
Cotransporter (Symport) using H+
Cause of hypercholesterolemia (고콜레스테롤 혈증)
Mutation in LDLR
- Incomplete dominance
- LL -> Normal
- Ll -> Found in later phase of life
- ll -> Found in early life stage
The most important ion in exocytosis
Ca++
What is Transcytosis
Macromolecules being passed through a cell and exocytosed into the ECM/adjacent cells
- Mother’s IgA in the colostrum through SI of an infant
What are M Cells
Microfold cells
Specialized epithelial cells in the intestine in the immune system
- Antigen transport into body -> lymphoid tissue
- IgA transport in infant SI (from colostrum)
Sizes of different cells (Smallest to Largest)
- Ribosome (not cell) - 10 ~ 10nm
- Virus - 50 ~ 100nm
- Filter paper (not cell) - 0.2µm
- Bacteria / Mitochondria - 1~2µm
- Eukaryotic Cells - 10~20µm
- Egg cell 100µm
Resolution (해상도)
The minimum distance (d) between to points for it to be recognized as to distinct points
Smaller d value means higher resolution
Difference between fungi and animal
Single cell/multi-cell vs multi-cell
Germ layer differentiation
배엽분화 (Germ Layer Differentiation)
Peptidoglycan Structure
N-acetylglucosamine + N-acetylmuramic acid + AA crosslink
B 1,4 glycosidic bond between NAM and NAG
Gram (+) Bacteria example
Staphylococcus aureus (황색포도상구균)
Streptococcus pneumoniae (폐렴구균) - G+ but does have outer lipd layer
Gram (-) example
Escherichia coli
B lactams mechanism
Acts on d,d-transpeptidase to block peptidoglycan formation
What does d,d-transpeptidase do
Forms the AA crosslink in peptidoglycan layer
Characteristics of Gram+
Multiple layers of peptidoglycan (~10)
Characteristics of Gram-
- outer membrane
- Lipopolysaccharide (LPS) -> endotoxin
LPS structure and endotoxicity
Lipid A + O-antigenic saccharide
Lipid A has endotoxicity
Characteristics of Gram +
- Thick peptidoglycan layer
- Teichoic acid / Teichuronic acid / monoaccharides (manose, galctose, arabinose) / Lipoteichoic acids
Bacteria that form endospore
Gram +
Bacillus anthracis (탄저균)
Clostridium botulinum
Gram dyeing Process
- Fixation - Heat or 70%etOH or 산알코올(?)
- Dye - Cristal Violet (+- both purple)
- Dye fixation - Lugol’s Iodine -> CVI complex
- Decolorization - Alcohol (+ purple / - no color)
- Counterstain - Safranin (+Purple / - pink
Cytosol: Palmitic acid 16:0
sER: changed to Stearic acid 18:0 or Oleic acid 18:1
Signaling Peptide
Signals ribosome-mRNA complex to move to rER to continue translation
N-glycosylation
Asn in the protein is glycosylated with saccharides on dolichol
N-glycosilation + Pi = ?
Lysosome protein
O-Glycosylation
In golgi
Ser/Thr glycosylated
Substrate-level phosphorylation
Glycolysis
- Phosphoenolpyruvate +ADP -> Pyruvate +ATP
- 1,3-biphosphoglycerate + ADP -> 3-phosphoglycerate +ATP
TCA
- GTP + ADP = GDP + ATP
Chemiosmotic Phosphorylation
- Use E from ETC to create H+ gradient
- Use H+ gradient to phosphorylate ADP
Photophosphorylation at photosystem / Oxidative phosphorylation at ETC
Glycolysis process
Describe glycolysis (not process)
- At Cytosol (ALL ORGANISMS)
- Glucose (C6) -> 2Pyruvate (2xC3) +2NADH +2ATP
- [ATP] increase inhibits glycolysis
- Invest 2ATP for 4ATP return
