BIO202 EXAM 1 Flashcards
(126 cards)
1
Q
Element
A
A substance that cannot be broken down by chemical reactions
2
Q
Atoms
A
The smallest unit of matter that retains properties of an element
3
Q
Trace elements
A
Required in minute amounts. Their lack can cause severe disorders
4
Q
Proton mass
A
1 Dalton
5
Q
Isotopes
A
Atomic forms of the same element with different number of neutrons (differ in mass)
6
Q
Electrons
A
Surround the nucleus and are located in energy levels. They have a charge of -1 and their mass is negligible in biology
7
Q
Neutrons
A
Located inside the nucleus. Have a neutral charge and have a mass of 1 dalton.
8
Q
Protons
A
Located in the nucleus. Have a charge of +1 and have a mass of 1 dalton. The atomic number is equal to the number of protons.
9
Q
Atomic mass
A
The # of protons + # of neutrons
10
Q
Atomic #
A
of protons
11
Q
Radioactive elements
A
Have specific and constant periods of decay called a “half-life”. They can serve as cytotoxic agents, introduce mutations in DNA, and can serve as biological tracers.
12
Q
Cytotoxic agents
A
Kill proliferating cells (treatment of cancer)
13
Q
How to radioactive elements typically induce mutations in DNA?
A
Large deletions
14
Q
How do radioactive elements serve as biological tracers?
A
Radioactive labeling of biological molecules (DNA, proteins, etc.), and following their fate in a cell or organism
15
Q
Energy
A
The ability to do work
16
Q
Potential energy
A
Energy stored in matter due to its location
17
Q
Covalent bonds
A
Involve the sharing of electrons. This can result in single, double or triple bonds. Usually require chemical reaction to break these bonds.
18
Q
Polar bonds
A
Unequal sharing of e-
19
Q
Non-polar bonds
A
Equal sharing of e-
20
Q
Ionic bonds
A
The complete transfer of valence electrons between atoms. Don’t usually require a chemical reaction to break them.
21
Q
Hydrogen bonds: Weak bond or strong bond?
A
Weak bond
22
Q
Vander Waals Forces: Weak bond or strong bond?
A
Weak bond
23
Q
Molecule
A
2 or more atoms held together by a covalent or ionic bond
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Q
The most electronegative atoms in biology
A
Nitrogen and Oxygen
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CH4
Bond type: Single, double or triple?
Polarity? Hydrophobic or hydrophillic?
Single bonds, non-polar, hydrophobic
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What's the difference between non-polar and polar covalent bonds?
In non-polar bonds, the electrons are equally dispersed. In polar bonds, electrons are shifted to the most electronegative atom.
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OH
Bond type: Covalent or ionic? Polarity?
Polar covalent bond
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Electronegativity
An atom's attraction for electrons
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What does a big difference in electronegativity result in?
Ionic bonds
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How are ionic bonds effected by their environment?
With salts, dry molecules have strong bonds and wet molecules have weak bonds.
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What types of bonds are most common in large molecules in the cell and why are they needed?
Weak bonds because they allow for transient (temporary) association with other molecules. Ex: signaling reactions.
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Hydrogen bonds
Occurs when one H bonded to one e- is attracted to another which is not covalently attached to them
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Van der Waals
The weakest of bonds. Molecules have slight attractions due to electron movement and unequal dispersion. These attractions occur even with non-polar covalent bonds.
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Chemical bonds
May occur within molecules to maintain conformation.
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What happens to chemical bonds during a chemical reaction?
They are broken and formed
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What are the 4 properties of water?
Cohesive behavior, ability to stabilize temperature, expansion upon freezing, and solvent versatility.
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Cohesive behavior of water
Plants can lift water up using capillary action. The hydrogen bonds in water give it adhesive and cohesive properties.
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What is an environmental benefit of water's expansion upon freezing?
It can float so life under the ice can survive in a lake during the winter. It doesn't allow large bodies of water to freeze all the way to the bottom.
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How is water able to stabilize temperature?
It has a high specific heat because it is hard to break many H-bonds. It absorbs the sun's energy and stores it, moderating climate. Ice has more H-bonds than liquid. When you form bonds you release energy and heat the environment. Cells are made mostly of water and we can adapt to temp changes.
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Solvent versatility of water
Versitile because is has polar bonds. Even non-ionic bonds can dissolve in water and it is a good solvent for biological solutions.
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Hydrophilic substances
Substances that dissolve in water. Usually ionic or polar. Some hydrophilic substances don't dissolve in water but they absorb it. (cotton)
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Hydrophobic substances
Cannot dissolve in water.
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Fuctional groups
components of organic molecules that are most commonly involved in reactions
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buffer
a substance that minimizes pH
changes by absorbing protons (H+) when
they are in excess and donating them when
they are depleted
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Simple sugars
Type of macromolecule ex: glucose
Sugars are carbohydrates; carbohydrates have a molecular formula in which (C)n(H2O)m => C:H:O ratio is n:(2:1)m
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Fatty acids
Fatty acids are sources of food (produce more energy
than glucose)
• Fatty acids are part of phospholipids (essential component
of membranes)
• Fatty acids are stored as fats (=triglycerides) (energy
sources) and as phospholipids (components of cell
membranes)
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If a fatty acid chain has no double bonds it is
saturated
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If a fatty acid chain has double bonds it is
unsaturated
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Structure of a phospholipid
Double bond in unsaturated fatty acid chain often bends. Resulting kink prevents close packing of phospholipids within the membrane. Has a hydrophillic head and hydrophobic tails (fatty acids).
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Sterols
Another major class of lipids. Function as components of the plasma membrane and are precursors of steroid hormones.
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Nucleotide functions
1. Energy carriers (ATP, GTP)
2. Signals (cAMP)
3. Subunits of DNA and RNA
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The 5 kinds of nucleotides are
Cytosine, thymine, uracil, adenine. and guanine
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What are pyrimidines and which nucleotides belong to this group?
They are 6-membered rings. (cytosine, thymine, and uracil)
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What are purines and which nucleotides belong to this group?
They are a 5-membered ring attached to a 6-membered ring. (Adenine and guanine)
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nucleoside
base + sugar. The base is at carbon 1 and carbons 3 and 5 are functionally very important.
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What are the differences between the bases in RNA and DNA?
In RNA Uracil is present. In DNA Thymine is present. Uracil lacks the methyl group at position 5.
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What are the differences between the sugars in RNA and DNA?
RNA has ribose and DNA has deoxyribose. Ribose has a carbonyl group and deoxyribose does not.
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nucleotide
A phosphate ester of a nucleoside. Usually esterification occurs at position 5 of a sugar (nucleotide = nucleoside-5`-phosphate) It could be 1, 2, or 3 phosphate groups.
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Transcription
The process of converting DNA to RNA by DNA-dependent RNA polymerase
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Translation
Converting RNA to proteins
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Translation results in
a specific polymer of amino acids (protein)
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Ribosomes
The organelle that reads the genetic code. It sets the correct reading frame (open reading frame) and moves along the length of mRNA adding 1 amino acid at a time. Amino acids are added by an adaptor.
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acceptor site
where the amino acid is bound
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Amino acids (Facts)
They are classified as polar (uncharged or charged) Basic (+) [in DNA binding proteins, NLS signals.] Acidic (-), or non-polar (often parts of hydrophobic membrane domains)
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Within a protein molecule N-C is a
peptide bond
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protein function
structure, storage, transport, hormones, receptors, contractions, defense, and enzymes
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4 levels of protein strucure
primary, secondary, tertiary, and quaternary
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primary protein structure
Only the sequence of amino acids within a protein. Can only be destroyed by chemical reactions. Only mutations can change the primary structure
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N-terminus
5' end
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C-terminus
3' end
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secondary protein structure
The chemical bonds in the peptide backbone. Folds and coils make up the secondary structure. Results from weak hydrogen bonds (Weakly positive H and weakly negative N and O)
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tertiary protein structure
Chemical bonds between side chains.They can be caused by 4 types of interactions: (Hydrogen bonds, Ionic bonds, Disulfide bonds (covalent), and Hydrophobic interactions
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Quaternary protein structure
Association of several protein subunits to form a more complex molecule.
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alpha-helix
A type of secondary structure wherea protein coil
| held together by hydrogen bonds every 4th peptide bond. Bonds are within the peptide backbone
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beta-helix
A protein chain folded on itself so that two regions are parallel to each other; these are held together by hydrogen bonds. They form very rigid structures
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The best way to determine a proteins secondary and tertiary structure.
x-ray diffraction analysis, which requires the protein to be crystallized
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Denaturation
The destruction of the secondary, tertiary, and quaternary structure
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endergonic reaction
energy of the reactants is smaller than the energy of the products
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exergonic reaction
energy of the reactants is greater than the energy of the products
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The catalytic cycle of an enzyme
An enzyme and substrate are available and the substrate binds to the enzyme. The substrate is then converted to products. Products are released and the active site is now free for another substrate to bind to it.
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What do enzymes do to the activation energy?
They lower it.
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What do enzymes to do the deltaG of a reaction?
Nothing. It remains the same.
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What does it mean when we say that enzymes are substrate specific?
They only catalyze specific reactions.
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Enzymes are usually ________ .
Proteins
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V(max)
The maximum reaction rate. The enzyme works at full capacity, usually when substrate is not limited.
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Is the hydrolysis of ATP exergonic or endergonic
exergonic
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Coupling
When endergonic reactions are driven by the energy released from exergonic reactions.
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ATP Cycle
The ATP cycle involves coupling. The Energy of ATP hydrolysis is used for anabolism. These are reactions that use energy to build complex molecules from simpler ones. (When adenine diphosphate becomes adenine triphosphate by obtaining a phosphate group.) Energy from catabolism is used for ATP synthesis. These are reactions that release energy by breaking complex molecules into simpler ones.
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Anabolic reactions
When energy is used to make a complex molecule from simpler ones
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Catabolic reactions
They release energy by breaking complex molecules into simpler ones
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Prokaryotic cells
Bacteria and cyanobacteria, which is blue-green algae. It has no nucleus. Their sizes range from 1-5um
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Eukaryotic cells
These include protists, fungi, plants and animals. The have a nucleus and are compartmentalized. They are larger cells that range from 10-100um.
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Why are cells so small?
A large surface area is needed for the cell to interact with the environment. Also, if a cell gets too big, the cell membrane would not be able to meet the demands of its volume.
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Why are cells compartmentalized?
To reduce diffusion distances and to separate "incompatible" reactions and their products.
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Chromatin
A complex of DNA and histones (proteins that package DNA). It is located in the nucleus
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Nucleolus
The site of assembly of immature ribosomes. It is located in the nucleus.
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Nuclear lamina
Supports the nuclear envelope. It is located in the nucleus.
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Nuclear envelope
Double membrane of the nucleus. It extends directly to the ER.
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Nuclear pore
Connection between the karyoplasm (or nucleoplasm) and cytoplasm. It is a large structure and it allows small molecules to diffuse into the nucleus. It selectively regulates transport of larger molecules. Nuclear import requires specific signals (NLS)
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karyoplasm
plasma inside the nucleus
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NLS
nuclear localization signals
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ribosomes
They synthesize proteins based on mRNA information. Ribosomes in the cell are either free or bound to the endoplasmic reticulum
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Endoplasmic reticulum
Make up more than half of the membranes in the cell. It consists of tubules and cisternae. It is directly connected to the nuclear envelope.
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Cisternae
sacs located in the ER
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Difference between rough ER and smooth ER.
Rough ER has attached ribosomes. Smooth ER is ribosome free.
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Smooth ER
Synthesizes lipids, metabolizes carbohydrates, synthesizes some hormones, and detoxifies drugs and poisons by adding -OH groups and making them more soluble.
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Rough ER
Synthesizes proteins that are to be exported or inserted into membranes. They modify proteins (Ex. acquire sugars and become glycoproteins) They produce their own membranes by adding phospholipids.
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Golgi apparatus
Membranous structure. It is the center for storage, modification, sorting, and transport of ER products. The "Cis-face" receives incoming vesicles from the ER and the trans-face sends off vesicles to other parts of the cell.
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What's in the vesicles of the golgi apparatus?
Proteins modified by the ER and golgi as well as modified phospholipids.
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Where do the vesicles go?
To specific parts of the cell.
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Lysosomes
Membrane vesicles filled with digestive enzymes (proteases and nucleases). They are found in animal cells. They have a pH of about 5.0.
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Hydrolytic enzymes of lysosomes
Are active at low pH and inactive at neutral pH of the cell cytosol.
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What happens if 1 lysosome breaks?
Its enzymes become inactive and cannot harm the cell.
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What happens if too many lysosomes break?
The cell dies. This is a mechanism of programmed cell death. (Autolysis)
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Lysosome functions
1. Degrade a recycle macromolecules
2. Digest food (in protazoa)
3. Cell self-distruction
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Central vacuole
The plant homolog of lysosome. It is a large central vesicle bound by a special membrane (tonoplast). Its functions include disposal/recycling, storage, and reduction in cell volume for faster diffusion
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Peroxisome (what)
A membrane-wrapped compartment which contains enzymes that transfer H from certain substrates to O, producing H2O2. Also contains other enzymes that convers H2O2 to H2O.
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Functions of peroxisome
Detoxification of alcohols and other compounds. Also, the breakdown of fatty acids.
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Mitochondria
The site of cellular respiration (Where most ATP is generated) It has a smooth outer membrane, an inner membrane that is infolded, and a matrix inside the inner membrane. It has its own DNA genome.
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What are the infolds on the inner membrane of mitochondria called?
Cristae
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What is cristae?
The infolds on the inner membrane of mitochondria
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Chloroplasts
Found in plant cells and they are green plastids. They are the site of photosynthesis, composed of a double membrane, narrow intermembrane space, and grana within stroma. They have their own DNA genome.
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grana
Stacks of thylakoids found in chloroplasts
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Stroma
fluid outside of thylakoids.
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True or false: chloroplasts have their own DNA
True
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Peptide bond
A chemical bond formed when the carboxyl group of one molecule reacts with the amino group of another molecule by hydrolization. It usually between amino acids.
