Midterm Flashcards
Lecture 2 ~ 8
2
Biology
Definition
Biology: science that studies life
2
6 Properties of Living Things
List them (probably with examples)
- Order
- Maintaining stable internal environment (homeostasis)
- Respond to external stimuli
- Positive response: Movement toward a stimulus
- Negative response: Movement away from a stimulus - Growth
- Reproduction
- Energy processing
2
What about viruses?
Are they alive?
- Most biologists think viruses arem’t alive
- But they are biological
2
The earliest observation of cells
3 stages(?) steps(?)
Leeuwenhoek: made good quality lens (not for cells though) and it became microscopes.
Robert Hooke: Observed cell walls under a microschope
Schleiden & Schwann: Oberserved cells and came up with cell theory
2
Cell Theory
List the 3 parts
- All organisms are made out of one or more cells.
- Cells are the basic structural & functional unit of all living organisms.
- All cells come from pre-existing cells.
2
Theory v.s. Hypothesis
Define them
Hypothesis: a testable/falsifiable predictions that attempts to explain an observation/phonomenon.
Theory: a general set of ideas that is intended to explain facts or events. (Evidence collected from hypothesis support theory.)
이거 또 틀리기만 해봐라
2
The Process of Science
(I don’t think it’s gonna be tested though) but there is 5 steps
- Make an observation
- Ask a question
- Form a hypothesis
- Make a prediction
- Test the prediction
(If it’s not testable… go back to 1 and just make more observation)
2
Where does the energy used to sustain the biosphere come ultimately come from?
Here comes the
SUN
2
Where energies are stored & how energies are earned/used
Where are energies stored? How plants/animals process energy?
Energy in living things are stored as chemical energy.
- Energy is stored in the bonds between the atoms of molecules.
For plants/photosynthetic organisms, light energy is converted to chemical bonds to put sugar (glucose) together.
For the living things that can’t do photosynthesis, they nom nom food/molecules to get energy.
2
Autotrophs
Heterotrophs
Define them
Authotrophs: Use abiotic sources of energy to produce complex molecules.
ex) Plants using light
Heterotrophs: MUST use the complex molecules produced by autotrophs* as an energy source
ex) Humans
3
Metabolic pathways
There is 2. Energy required? or energy released?
Anabolic: Small molecules are built into large ones
-> Energy required
Catabolic: Large molecules are broken down into small ones
-> Energy released
3
4 Types of chemical bonds
- Ionic bonds: When the elements donates & accepts electrons to each other.
- Covalent bonds: electrons are shared between atoms to form a strong association.
- Nonpolar covalent bond: all the atoms share the electrons equally.
- Polar covalent bond: The electrons shared spend more time closer to 1 nucleus to the other one. It results slightly (+) & (-) charged atoms.
3. Hydrogen Bonds (polar covalent): form between H atoms and other polar covalent molecules.
- Unique properties of water & DNA/proteins - Van der Waals Interaction: weak interactions between molecules that occur between polar covalently bound atoms in different molecules.
3
Why is carbon so important in living things?
C can bond with up to 4 other atoms to form diverse molecules with elabroate structures.
3
Organic compounds & carbon fixation
Define. Alsom what are the exceptions?
Organic compounds: carbon containing compounds.
- CARBON BONDED TO OTHER C OR H
- CO & CO2 ARE NOT ORGANIC!!!
Carbon fixation: conversion from inorganic compound -> organic molecules useful for living things
- It takes a lot of energy to do it
3
4 Major Organic Compounds
Just list them cuz they will each have their own separate slide.
- Lipids
- Carbohydrate
- Nucleic Acids
- Proteins
3
Lipids
Describe.
- FATS (fats, oils, waxes, steroids)
- Important energy source
- Long chains of C & H
- The C&H chains are neutral in charge
- Hydrophobic (cuz they’re non-polar)
- Only the small portion at the end with the only Oxygen can interact with water.
- Builds hormones
- Lipids in water arranges themselves in a way to “shield” the hydrphobic portions away from water
- Phospholipids: form the basis of biological membranes (helps maintain the stable internal envrionment)
얘네 organic compounds 4개 중에 유일하게 hydrophobic
3
Carbohydrates
- SUGAR
- Provides energy to our body
- Monosaccharides: simple sugars (glucose)
- > this one is a monomer
- Major ones have 6 carbon atoms
- Hydrophilic! (cuz sugar dissolves in water lmao)
3 - 4
Nucleic Acids
- Polymers of nucleotide
- It stores genetic info in cells.
- DNA&RNA
- There are 5 kinds of nucleotides and each nucleic acid contains 4 of them (A,C,T,G,U)
Structure: - Base: determines what kind of nucleotide it is (The only differences between different types of nucleotide is the base).
- Nucleoside: Sugar + base
- Nucleotide: sugar + base + 1~3 phosphates
nucleotide가 nucleic acid 되려면 4개 필요
4
DNA vs RNA
- Sugar is different
- RNA = Ribose, DNA = Deoxyribose
- This extra oxygen in DNA makes it more stable than RNA
- RNA is less stable but breaks down much quicker - Types of nucleotides
- RNA: U, DNA: T
4
Base pairing & DNA structure
and what bonds
- Each nucleotide specifically pairs with another by forming HYDROGEN BOND
- The # of bonds affects the trength of interaction, 즉, G & C가 부수기 더 어려움.
- New nucleotides are added at 3’ end, forming COVALENT BOND
- The complementary strand runs in the opposite direction (만약 5->3이면 3->5)
same strend = covalent
different strend = hydrogen
makes sense because 다른 strend는 어차피 나눠질거 그렇게 strong한 bond가 아니어도 상관없음
4
Base pairing & RNA structure
- RNAs can fold in different ways that perform specific functions.
- The sequence of nucleotides determines RNA molecule’s structure.
4
ATP
Define & 3 steps of how it is used as energy
ATP: transfers energy from broken down sugars amd fats to various cellular functions.
- It has 3 phosphates.
1. The last phosphate is removed and gets transferred to whatever function it needs
(ATP becomes ADP + phosphate)
2. We nom nom food and that energy gets digested and broken down.
3. That digested energy is used to put ADP and phosphate back together to ATP!
(and then over and over again)
3 - 4
Proteins & Amino acids
Define. Describe characteristics (그냥 생각나는 대로 막 뱉어)
- Amino acids: fundamental unit that make up proteins
- Peptides: short chains of amino acids (<30)
- Protein: Polymers of amino acids
- Most diverse in function in the cell
- About 20 kinds of relevant amino acids in real life.
- Each amino acid monomer has a unique “side chain”
4
How amino acids join
what bond?
- They form a covalent bond
- Also have directionality (new amino acids will be added to the c-terminus)
4
Enzymes
Define & describe
- It is a type of protein that speeds up reactions in the cell
- Catalysts
- It helps hold pairs of glucose together while they react to speed it up.
4
What determines a protein’s shape & function?
- Type
- What amino acids are chained together? - Sequence
- What order of amino acids?
5
The “Typical” Cell
At a minimum, all cells must have 4 components
- Plasma membrane
- DNA
- Cytoplasm
- Ribosomes
5
What are the 2 distinct kinds of cells?
- Prokaryotic cells
- Eukaroytic cells
5
3 Domains of life
- Bacteria
- Archaea
- Eukarya
Procaryote iteself is NOT A Domain!
Domains are 1 higher than kingdom
5
Prokaryote vs Eukaryotes
There’s 4
- Eukaryotic cells are more complex & bigger
- Eukaryotic cells have nucleus
- The common ancestor or living things looked more like prokaryotes.
- Eukaryotes have membrane bound organelles (They have phospolipids layered membranes around them)
5
Do biological membranes let things inside cells?
It’s semi-permiable.
aka only let things in depending on the needs of the cell.
5
What do each component does in membrane?
There’s 3 but 2 more (?)
- Lipids
- Phospolipids: comprises most of the membrane
- Cholesterol: fluidity/flexibility of the membrane - Proteins - it does so many things
- Channels: allows materials to enter/exit the cell
- Emzyes: speed reactions near the membrane
- Receptors: respond to stimuli
- Attachment points for structural components - Carbohydrates (only plasma membrane)
- helps other cells recognize/identify each other.
5
Plasma membrane
What’s the function
It separates the outside world from the inside cell.
5
Things that can enter the plasma membrane without any struggle
There’s 2
- Gases & Hydrophobic molecules (CO2, CO, O2)
- Small uncharged polar molecules (H2O)
5
Things that can’t get through or need assistance
2
- Large uncharged polar molecules
- Charged ions
5
Passive Transport & concentration gradient
Define it & 2 types of concentration gradient
Passive Transport: No energy is required to get these substances inside the cell.
Concentration ogradient: The substances move away from concentrated spots so it is well spread out.
- Diffusion
- Osmosis
5
Diffusion
Define it & explain how it works
Diffusion: Dissolved materials moving areas of high concentration -> lower concentration
5
Facilitated Transport
Define it & example
- Larger substances require assistance to pass through.
- ex) glucose needs protein channel to let diffusion happen.
- It’s part of passive though.
5
Osmosis
Define it & describe how it happens
Osmosis: water moving from an area of low concentration to high concentration
-> it’s about movement of water
-> If the substances are too big to do diffusion
5
Active Transport
define it & give example & Endocytosis
Active Transport: Consume ENERGY to move the substances in & out of the cell
-> Require transport protein!
Ex) Protons (H+) are against concentration gradient. Then ATP provides energy that’s required by sending the 1 phosphate
Endocytosis: absorb nom nom too large substances into the cell by etrapping the substance within the cell membrane.
1. Phagocytosis
- Plant cells can’t do it cuz of the cell walls
2. Pinocytosis
3. Receptor-mediated endocytosis
6
Endosymbiotic theory
Explain & give 3 evidences
- Eukaryote nom nom bacterium as usual
- But it didn’t get digested and escaped to the cytoplasm!
- Those became chloroplasts & mitochondria
Evidences:
1. Mito & chloro look like & divide like bacteria
2. Divide “independently” of its host cell
3. Still maintain a genome?! (their own dna)
7
Genome vs Gene
Define them
Genome: All the genetic material in an organism passed from parent -> offspring
Gene: A hereditary unit passed from parent to offspring. It tells cells how to function
- Gene is part of genome
- mRNA is used to guide proetin production
7
3 Steps of gene expression
Just list them for now
- DNA replication
- Transcription
- Translation
7
DNA Replication
- Untwist the DNA (separate it)
- Add complementary nucleotides for each strend from 3’ end.
- DNA Replication is semi-consenative
- 절발만 original로 남고 반은 새로 synthesized 된 거
7
Genes
Describe the 5 facts
- Unit of heredity
- Segments of DNA
- They are transcribed into RNA
- Humans have around 20,000 genes!
- Encode proteins
7
The Central Dogma of Molecular Biology
DNA? RNA? PROTEIN?
- DNA: Permanent storage of the information (언제든지 꺼내서 이용하셈)
- Transcription - RNA: Temporary relay of the information
- Translation - Protein: Interpretation of the information
7
Anatomy of a Gene
Promotor, Terminator, upstream, downstream
Promotors: Regions where RNA polymerases (enzymes that make RNAS) bind before transcription
Terminators: Regions where RNA polymerases detach to end transcription
Upstream: Promotor side 5’
Downstream: Terminator side 3’
7
Transcription
Definition, where it happens, 3 steps
Transcription: Replicating DNA into RNA.
Where it happens?
- Prokaryotes: cytoplasm
- Eukaryotes: nucleus
3 steps:
1. Initiation
- Transcription starts at ‘transcription start site’ (right next to the promotor)
- the DNA strend gets splited and RNA pol gets ready to bind with the promotor
- Enhancers: Make the transcription happen more often
- Repressors: Make the transcription happen less frequently
2. Elongation
- RNA pol is added to 3’
- Template strend: the strend that RNA uses as a guide line (And then there is non template strend)
3. Termination
- Terminator contains a sequence that results in the end of transcription. (AAAAAA)
7
3 Types of RNAs
- rRNA: Ribosomal RNA
- tRNA: Transfer RNA
- mRNA: Messanger RNA
Premature RNAs needs modification though
7
RNA modification methods to become a mature RNA (mostly mRNA rn)
There’s 3!
- RNA splicing
- 5’ capping
- Poly-adenylating 3’ tails
8
Translation
Define & what is codon? Where it happens & & roles of each rnas 3 steps
use reading frame, anticodon
Translation: mRNA is translated into functional proteins
Where it happens?
- Prokaryotes: Cytoplasm
- Eukaryotes: Cytoplasm (ribosomes)
**mRNA: ** It messages guiding template of how amino acids should be chained together in a specific sequence
**Codons: ** “Words” made of 3 nucleotides each
**Ribosomes, rRNA: ** Ribosomes are made of proteins & rRNAs.
rRNA is an enzyme that forms the covalent bond between the 2 amino acids.
Ribosomes have 2 components: Large unit, subunit
**tRNA: ** What actually carry amino acids to the ribosome.
- Anticodon: 3 nucleotide sequence on a tRNA that base paris with the codons in an mRNA.
3 Steps:
1. Initiation
- tRNA & small ribosomal subunit start to interact and scan to see the the start codon (AUG)
2. Elongation
- Second tRNA enters to the A site
- They BOND with the first tRNA (c-terminus of the first Met)
- Reading frame: way of dividing the sequence of nucleotides in DNA/RNA into consecutive non-overlapping triplet codons.
3. Termination
- Reach to the stop codon
- Amino acid chain get cut off in the p site.
ending codon is not part of amino acid!
8
Think quick: What’s the anticodon for Trp?
Trp: UGG
3’ACC5’
8
if the things break
3 possible ways
- Frame shift: if 1 nucleotide suddenly deleted, the reading frame changes by changing its amino acid sequence after that point (ig we’ll find another stop codon at some point)
- If 1 nucleotide changes to a new one (AUA-> AAA)
-> Protein can’t function properly anymore :( - If the changed codon still codes for the same amino acid:
-> It stays the same :D
-> Silent mutation
