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BIO130 > Test 1 > Flashcards

Test 1 Flashcards

1
Q

Central dogma

A
  • the flow of info from DNA to RNA to protein
  • fundamental process
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2
Q

How do cells self-replicate?

A
  • DNA encodes info that leads to making proteins (sequence info)
  • proteins catalyze replication of DNA and transcription of RNA and participate in translation of RNA into proteins and many other chemical reactions in body (catalytic activity)
  • feedback loop b/w proteins and polynucleotides creates
  • underlies the self-reproducing behaviour of living things
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3
Q

Viruses are non-living things.

A

TRUE
- cannot self-replicate
- they reproduce by parasitizing the reproductive machinery of invaded cells to make copies of themselves
- chemical zombies: inert and inactive outside host cell

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4
Q

Transmission electron microscope

A
  • type of electron microscope used to look at thin sections of tissue (must be very thin bc of small wavelength of electrons)
  • transmits a beam of electrons rather than a beam of light (like a light microscope) through sample
  • contrast is usually made by staining the specimen with electron-dense heavy metals
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5
Q

Scanning electron microscope

A
  • scatters electrons off surface of sample
  • used to look at surface detail of cells and structures
  • specimen is coated with very thin film of heavy metal
  • magnetic coils act as lenses that bring focus on specimen
  • useful for 3D imaging
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6
Q

What techniques can be used to determine the precise positioning of atoms within the 3D structure of protein molecules and complexes?

A
  • xray crystallography
  • cryoelectron microscopy
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7
Q

Bacteria

A
  • simplest structure, only essentials
  • no organelles other than ribosomes (no nucleus to hold DNA)
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8
Q

Prokaryotes

A
  • organism whose cells do not have nucleus
  • shape: typically spherical, rodlike, or corkscrew
  • very small
  • often have touch protective coat (or cell wall) around plasma membrane
  • inside cell is a single compartment containing cytoplasm and DNA
  • cells reproduce quickly
  • most diverse and numerous cells on earth
  • most are single-celled organisms
  • some join together to form chains, clusters and organized multicellular structures
  • almost any organic, carbon-containing material can be used as food by bacteria
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9
Q

Eukaryotes

A
  • organisms whose cells have a nucleus
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10
Q

Why can prokaryotes evolve fast?

A
  • large numbers
  • rapid proliferation
  • ability to exchange bits of genetic material by a process akin to sex
  • thus they get ability to use new food source or resist being killed by new antibiotic
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11
Q

In terms of chemistry, prokaryotes are the most diverse class of cells on planet

A

TRUE

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12
Q

Some prokaryotes can live on entirely inorganic substances

A

TRUE
- they can get their carbon from CO2 in atmosphere, their nitrogen from atmospheric N2 and oxygen, hydrogen, sulfur and phosphorus from air, water and inorganic materials

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13
Q

In a way, plants depend on bacteria for photosynthesis.

A

TRUE
- plants unaided by bacteria cannot capture N2 from atmosphere
- they can still capture energy from sunlight and carbon from atmospheric CO2
- PLUS, chloroplasts evolved from photosynthetic bacteria that planted itself inside the cytoplasm of a plant cell ancestor long ago

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14
Q

Two domains of the class of prokaryotes.

A
  • bacteria (most prokaryotes)
  • archaea (found in environments that are too hostile for most other cells, such extreme environments resemble the harsh conditions that must have existed on primitive earth, with no oxygen)
  • thought to have diverged from common prokaryotic ancestor about 3.5 bil years ago
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15
Q

Eukaryotic cells

A
  • in general, bigger and more elaborate than prokaryotes
  • some live independently as single-celled organisms (e.g. amoebae and yeast), others in multicellular orgs
  • have a nucleus, which goes hand in hand with having other organelles (most are membrane-enclosed and common to all eukaryotic orgs)
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16
Q

Nucleus

A
  • info store of cell
  • usually the most prominent organelle in eukaryotic cell
  • enclosed within 2 concentric membranes that form nuclear envelope
  • contains molecules of DNA (most of DNA is in nucleus)
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17
Q

Mitochondria

A
  • generate usable (chemical) energy from food molecules
  • present in all eukaryotic cells
  • can vary in size and shape
  • among the most conspicuous organelles in cytoplasm
  • worm shaped structures with branching/folded/convoluted networks in inner membrane of organelle
  • function was discovered by breaking open cells and spinning its fragments in a centrifuge (separates organelles according to size and density) and then tested for which chemical processes they could perform
  • harness energy from oxidation of food molecules to produce adenosine triphosphate (ATP)
  • consumes oxygen and releases CO2 while making ATP so process is called cell respiration
  • without mitochondria, cells wouldn’t be able to use oxygen to extract required energy
  • contain their own DNA and reproduce by dividing
  • resemble bacteria and many ways
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18
Q

ATP

A
  • adenosine triphosphate
  • basic chemical fuel that powers most of cell’s activities
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19
Q

Why are mitochondria thought to have evolved from bacteria?

A
  • are thought to derive from bacteria that were engulfed by some ancestor of present-day eukaryotic cells
  • created a symbiotic relationship in which host eukaryote and engulfed bacterium helped each other survive and reproduce
  • almost certain that aerobic bacteria was engulfed by an archaea-derived, early anaerobic eukaryotic cell and survived inside it, living in symbiosis with their host
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20
Q

Inner membrane of mitochondria

A
  • inner membrane contains most of proteins responsible for energy production
  • it is highly folded to provide a large surface area for this activity
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21
Q

Chloroplasts

A
  • capture energy from sunlight
  • large, green organelles that are found in cells of plants and algae but not in animals or fungi
  • in addition to 2 surrounding membranes (like mitochondria) they possess internal stacks of membranes with green pigment chlorophyll
  • carry out photosynthesis, allowing plants to get energy directly from sunlight
  • allow plants to produce food molecules and oxygen that mitochondria use to generate chemical energy
  • contain their own DNA
  • reproduce by dividing in 2
  • are thought to have evolved from bacteria
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22
Q

Double membrane of mitochondria evolution

A
  • double membrane of present-day mitochondria is thought to have been derived from plasma membrane and outer membrane of engulfed bacterium
  • membrane derived from plasma membrane of engulfing ancestral cell was ultimately lost
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23
Q

Photosynthesis in chloroplasts

A
  • chloroplasts trap sunlight energy in their chlorophyll molecules and using this energy to drive the manufacture of energy-rich sugar molecules
  • in the process, they release oxygen as a molecular by-product
  • ## plant cells can then extract this stored chemical energy when they need it by oxidizing sugars and their breakdown products, mainly in mitochondria (as animal cells)
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24
Q

How did chloroplasts evolve?

A
  • evolved from bacteria, just like mitochondria
  • photosynthetic bacteria was engulfed by an early aerobic eukaryotic cell that already contained mitochondria
  • loss of membrane derived from plasma membrane of the engulfing early eukaryotic cell occurred after photosynthetic bacterium was engulfed
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25
Q

Endoplasmic reticulum (ER)

A
  • an irregular maze of interconnected spaces enclosed by a membrane
  • site where most cell membrane components and materials destined for export from cell are made
  • an organelle
  • enormously enlarged in cells that are specialized for secretion of proteins
  • produces many of the components of a eukaryotic cell
  • is continuous with membranes of nuclear envelope
  • mammalian pancreatic cell has vast amounts of ER, which is specialized for protein secretion
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26
Q

Rough ER vs smooth ER

A
  • rough ER is ribosome-coated ER
  • smooth ER does not have ribosomes bound to it
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27
Q

Ribosomes

A
  • structures that translate RNAs into proteins
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28
Q

Golgi apparatus

A
  • stacks of flattened, membrane-enclosed sacs
  • several stacks can be present in a cell
  • modifies and packages molecules made in ER that are destined to be secreted from cell or transported to another cell compartment
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29
Q

Lysosomes

A
  • small, irregularly shaped organelles
  • intracellular digestion occurs here
  • releases nutrients from ingested food particles into cytosol
  • breaks down unwanted molecules for either recycling within the cell or excretion from cell
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30
Q

Peroxisomes

A
  • small, membrane-enclosed vesicles
  • provide a sequestered environment for a variety of reactions in which hydrogen peroxide is used to inactivate toxic molecules
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31
Q

Transport vesicles

A
  • membranes form many types of small transport vesicles
  • they ferry materials between one membrane-enclosed organelle and another to allow the continual exchange of materials
  • they pinch off from membrane of one organelle and fuse with another
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32
Q

Cytosol

A
  • the cytoplasm that fills the space outside of organelles
  • concentrated aqueous gel of large and small molecules
  • part of cytoplasm that is not contained within intracellular membranes
  • contains a host of large and small molecules
  • behaves like a water-based gel because of the very crowded molecules
  • site of many chemical reactions that are fundamental to cell’s existence
  • early steps in breakdown of nutrient molecules take place in cytosol
  • proteins are made by ribosomes in cytosol
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33
Q

Endocytosis

A
  • process in which portions of plasma membrane tuck inward and pinch off to form vesicles that carry material captured from the external medium into the cell
  • import extracellular materials
  • endocytosed material is first delivered to membrane-enclosed organelles called ENDOSOMES
  • animal cells can engulf very large particles, or even entire foreign cells, by this process
  • continuous process
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34
Q

Exocytosis

A
  • reverse process of endocytosis
  • vesicles from inside the cell fuse with plasma membrane and release their contents into external medium
  • secretion of intracellular materials
  • most of hormones and signal molecules that allow cells to communicate with one another are secreted from cells by exocytosis
  • continuous process
35
Q

What is the largest single compartment in most cells?

A

Cytosol

36
Q

Cytoskeleton

A
  • responsible for directed cell movements
  • a network of protein filaments that can be seen criss-crossing the cytoplasm of eukaryotic cells
  • long, fine filaments that are often seen to be anchored at one end to plasma membrane or to radiate out from central site adjacent to nucleus
  • work together with other proteins that attach to them, form a system of girders, ropes, and motors
  • gives the cell its mechanical strength, controls its shape and drives/guides its movements
  • governs internal organization of cell and its external features
  • necessary to the tough-walled plant cell and flexible animal cell
  • is a dynamic jungle of protein ropes that are continually being strung together and taken apart
  • filaments can assemble and disappear in a matter of minutes
37
Q

3 major filament types of cytoskeleton

A
  • actin filaments (thinnest of filaments, abundant in all eukaryotic cells but especially abundant in muscle cells where they serve as central part of machinery responsible for muscle contraction)
  • microtubules (thickest filaments, called microtubules bc they have form of minute hollow tubes. In dividing cells, they become reorganized to help pull duplicated chromosomes apart and distribute them equally in 2 daughter cells)
  • intermediate filaments (intermediate thickness, serve to strengthen most animal cells)
38
Q

Most ancient function of cytoskeleton

A
  • its role in cell division
  • bacteria contain proteins that also form filaments and play a part in cell division that are distantly related to those that form cytoskeletal elements involved in eukaryotic cell division
39
Q

Motor proteins

A
  • use energy stored in ATP molecules to trundle along filaments, carrying organelles and proteins throughout cytoplasm quickly
40
Q

Cytosol is static

A

FALSE
- large and small molecules that fill space of cell are knocked around and hitting one another by random thermal motion
- cytoskeleton is constantly moving around

41
Q

Eukaryotic cells are typically 10 times the length and 1000 times the volume of prokaryotic cells.

A

TRUE

42
Q

According to one theory, the ancestral eukaryotic cell was a…

A
  • predator that fed by capturing other cells
  • such a way of life requires a large size, flexible membrane and a cytoskeleton to help the cell move and eat
  • nuclear compartment may have evolved to keep DNA segregated from the physical and chemical components, allowing for a more delicate and complex control of the way cell reads out its genetic info
43
Q

Where did eukaryotes come from?

A
  • eukaryotic, bacterial and archaean lineages diverged from one another more than 3 bil years ago
  • some time later, eukaryotes are thought to have acquired chloroplasts
  • mitochondria are essentially the same in plants, animals and fungi and were therefore presumable acquired before these lines diverged about 1.5 bil years ago
44
Q

Protozoans

A
  • class of free-living, motile, unicellular organisms
  • possess common behaviour to prey upon and swallow other cells
  • not all are predators
  • can be photosynthetic or carnivorous, motile or sedentary
  • anatomy is often elaborate and includes structures like sensory bristles, photoreceptors, beating cilia, stalklike appendages, mouthparts, stinging darts and musclelike contractile bundles
  • can be as intricate and versatile as many multicellular organisms
  • referred to as microorganisms bc they can only be seen with a microscope
45
Q

Model organisms

A
  • organisms/cells studied by biologists in depth to gain a deep understanding of them and then be pooled into a greater knowledge to understand other species/organisms
  • workings of the bacterium E. coli are understood the best in molecular terms (knowledge of the fundamental mechanisms of life came from it)
46
Q

In vitro vs in vivo

A
  • in vitro: “in glass”, experiments using cultured cells, in a culture dish, bc cultured cells are maintained in controlled environment, they are accessible to study in ways that are often not possible in vivo (e.g. exposing to hormones or growth factors)
  • in vivo: “in the living”, experiments on intact organisms
47
Q

Many cells, not all, including those harvested from humans, continue to display the differentiated properties appropriate to their origin when grown in culture.

A

TRUE
- e.g. embryonic heart muscle cells contract spontaneously, nerve cells extend axons

48
Q

Organoids

A
  • certain human embryo cells can be coaxed into differentiating into multiple cell types which can self-assemble into organlike structures that closely resemble a normal organ
  • can be used to study developmental processes and diseases
49
Q

Water accounts for 70% of a cell’s weight

A

TRUE
- most intracellular reactions occur in an aqueous envi

50
Q

Hydrophobic vs. hydrophilic

A
  • hydrophobic: “water-fearing”, uncharged molecules that form few or not H-bonds, do not dissolve in water
  • hydrophilic: “water-loving”, carry a + or - charge, mix well with water bc they can form H-bonds with their polar bonds
51
Q

The four types of weak chemical interactions important in biology in order of decreasing strength.

A
  • covalent (sharing)
  • noncovalent: ionic bond
  • noncovalent: hydrogen bond
  • noncovalent: van der Waals attraction
  • decreasing strength, increasing length of bond
52
Q

Amino acids

A
  • small organic molecules
  • possess a carboxylic acid group and an amino group, both attached to a central carbon atom
  • the carbon also carries a specific side chain
  • identity of side chain distinguishes the dif amino acids
  • used by cells to build proteins
  • in a cell, free amino acids exist in their ionized form
  • when incorporated into a polypeptide chain, the charges on their amino and carboxyl groups are lost
  • 20 dif types of amino acids found in proteins
  • all amino acids (except glycine) exist as optical isomers termed D- and L- forms
  • only L-forms are ever found in proteins (origin/evolution of this exclusive use is unknown)
  • D-amino acids occur as part of bacterial cell walls and in some antibiotics, D-serine is used as a signal molecule in brain
  • 5 of 20 amino acids have side chains that form ions in solution and can therefore carry a charge, others are uncharged
  • some are polar and hydrophilic, some are nonpolar and hydrophobic
  • collective properties of amino acid side chains underlie all the diverse and sophisticated functions of proteins
53
Q

One defining property of amino acids

A
  • they all possess a carboxylic acid group and an amino group, both attached to a central carbon atom
54
Q

Proteins

A
  • polymers made of amino acids which are joined head-to-tail in a long chain that folds up in a 3D structure that is unique to each type of protein
  • perform most of cell’s functions
  • serve as building blocks for cell structures
  • form the enzymes that catalyze chemical reactions in cell
  • regulate activity of genes
  • enable cells to move and communicate with one another
55
Q

Peptide bond

A
  • covalent bond b/w two adjacent amino acids in a protein chain
  • formed by condensation reactions that link one amino acid to the next
56
Q

Polypeptide

A
  • chain of amino acids linked by peptide bonds
  • regardless of the specific amino acids from which it is made, the polypeptide always has an amino group (NH2) at one end (its N-terminus) and a carboxyl (COOH) group at its other end (C-terminus)
  • this difference in the 2 ends gives a polypeptide a definite directionality, a structural polarity
  • sequence is always read starting from the N-terminus
57
Q

Nucleotides

A
  • subunits of DNA and RNA
  • DNA and RNA are built from nucleotides
  • nucleotides consist of a nitrogen-containing ring compound linked to a 5 carbon sugar that has one or more phosphate groups attached to it
  • the sugar can be either ribose (ribonucleotides) or deoxyribose (deoxyribonucleotides)
  • nitrogen containing rings are referred to as bases
  • have a fundamental role in storage and retrieval of biological info
  • serve as building blocks for construction of nucleic acids
  • linear sequence of nucleotides in DNA or RNA molecule encodes genetic info
58
Q

Why are nitrogen containing rings of nucleotides referred to as bases?

A
  • under acidic conditions, they can each bind a proton and thereby increase concentration of hydroxide ions in an (aq) solution
59
Q

The 5 different types of nucleotide bases

A
  • cytosine (C), thymine (T), uracil (U): pyrimidines bc they derive from a 6- membered pyrimidine ring
  • guanine (G) and adenine (A): purines, which bear a second, 5-membered ring fused to the 6-membered ring
  • each nucleotide is named after the base it contains
60
Q

Nucleoside

A
  • a base plus its sugar, without any phosphate group attached
  • nucleoside di- and triphosphates can act as short-term carriers of chemical energy
61
Q

Adenosine triphosphate

A
  • ATP
  • above all other nucleosides
  • a ribonucleoside triphosphate
  • participates in transfer of energy in metabolic reactions
  • formed through reactions that are driven by the energy released from the break-down of food
  • its 3 phosphates are linked in series by 2 phosphoanhydride bonds
  • rupture of these phosphate bonds by hydrolysis releases large amounts of free/useful energy
  • terminal phosphate group is usually split off or transferred to another molecule to release energy that can be used to drive biosynthetic reactions
62
Q

ATP synthesis

A
  • synthesizes from ADP and inorganic phosphate and it releases energy when it is hydrolyzed back to ADP and inorganic phosphate
  • energy required for ATP synthesis is derived from either the energy-yielding oxidation of food (animal cells, fungi and some bacteria) or the capture of light (in plant cells and some bacteria)
63
Q

Nucleic acids

A
  • long polymers in which nucleotide subunits
  • are linked by the formation of covalent phosphodiester bonds b/w the phosphate group attached to the sugar of one nucleotide and hydroxyl group on the sugar of the next nucleotide
64
Q

How are nucleic acid chains synthesized?

A
  • synthesized from energy-rich nucleoside triphosphates by a condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation
65
Q

2 main types of nucleic acids

A
  • ribonucleic acid (RNA): based on sugar ribose, contain bases A, G, C, U
  • deoxyribonucleic acid (DNA): based on deoxyribose in which the hydroxyl group at the 2’ position of the ribose carbon ring is replaced by a hydrogen, contain bases A, G, C, T.
  • differ in the type of sugar contained in their sugar-phosphate backbone
66
Q

RNA

A
  • ribonucleic acid (RNA): based on sugar ribose, contain bases A, G, C, U
  • usually occurs in cells in the form of single-stranded polynucleotide chain
  • single stranded
  • is usually more transient carrier of molecular instructions
67
Q

DNA

A
  • deoxyribonucleic acid (DNA): based on deoxyribose in which the hydroxyl group at the 2’ position of the ribose carbon ring is replaced by a hydrogen, contain bases A, G, C, T
  • essentially a long polymer composed of 4 types of nucleotide subunits
  • almost always in form of a double-stranded molecule
  • structure of DNA provides mechanism for heredity
  • DNA double helix is composed of 2 polynucleotide chains that run in opposite directions (antiparallel, have opposite chemical polarities) and are held together by H-bonds b/w bases of the 2 chains
  • its more stable, H-bonded helix acts as a long-term repository for hereditary info
  • carrier of the cell’s genetic info
  • structure of DNA is what suggested how DNA encodes, copies and passes on instructions
  • nucleotide bases on inside of DNA double helix, sugar-phosphate backbones on outside
  • the antiparallel strands twist around each other to form a double helix
  • twisting also contributes to energetically favourable conformation of DNA double helix
68
Q

Complementary base-pairing

A
  • ability of bases in dif nucleic acid molecules to recognize and pair with each other by H-bonding
  • G with C (3 H-bonds form)
  • A with T or U (2 H-bonds form)
  • underlies all of heredity and evolution
  • enables base pairs to be packed in most energetically favourable arrangement inside double helix
  • with such pairing, each base pair has same width, holding the backbones an equal distance apart along DNA molecule
  • for each base pair to fit together within double helix, the 2 strands must run antiparallel
69
Q

Dif ends of DNA molecule (5’ vs 3’ end)

A
  • bc bonds link specific carbon atoms in the sugar ring (known as 5’ and 3’ carbon atoms) one end of a polynucleotide chain, the 5’ end, has a free phosphate group and the other, the 3’ end, has a free hydroxyl group
  • sequence is always read from the 5’ end
70
Q

Phosphates

A
  • are normally joined to C5 hydroxyl of the ribose or deoxyribose sugar (designated 5’)
  • mono-, di- and triphosphates are common
  • 1 P group in AMP (adenosine monophosphate)
  • 2 P groups in ADP
  • 3 P groups in ATP
  • phosphate makes a nucleotide negatively charged
71
Q

Pentose

A
  • a five carbon sugar
  • 2 kinds of pentoses are used: B-D-ribose used in RNA, B-D-2-deoxyribose used in DNA
72
Q

UDP

A

uridine diphosphate

73
Q

dAMP

A

deoxyadenosine monophosphate

74
Q

Nucleoside vs. nucleotide

A
  • nucleoside: base + sugar
  • nucleotide: base + sugar + phosphate
75
Q

Base-nucleoside-abbreviation of nucleic acid bases

A

adenine - adenosine - A
guanine - guanosine - G
cytosine - cytidine - C
uracil - uridine - U
thymine - thymidine - T

  • the 4 of them (other than uracil) make up the genetic code
76
Q

What does genetic info primarily consist of?

A
  • instructions for making proteins
77
Q

Chromosomes

A
  • named from Greek word “chroma” meaning “color” bc of their staining properties
  • contain both DNA carries gen info of cell) and protein (pack and control the very long DNA molecules)
  • determine inherited traits and genes
78
Q

Why does each DNA strand have a chemical polarity?

A
  • nucleotide subunits in DNA strand are held together by phosphodiester bonds that link 5’ end of one sugar with 3’ end of next
  • bc ester linkages to the sugar molecules on either side of bond are different, each strand has a polarity
  • polarity is indicated by referring to one end as 3’ end and other as 5’ end
  • in middle of molecule, where the strands are bonded, the charges are cancelled
79
Q

How many base pairs per helical turn of DNA? In which direction does the helix wind?

A
  • 10
  • it is a right-handed helix
80
Q

Why do organisms differ from one another?

A
  • bc their respective DNA molecules have dif nucleotide sequences and so carry dif biological messages
  • each base (A, T, C or G) spells out a biological message, info is encoded using them
81
Q

Grooves in double helix

A
  • coiling of 2 strands around each other creates 2 grooves in double helix
  • major groove: wider/longer one
  • minor groove: smaller one
82
Q

Gene expression

A
  • process by which nucleotide sequence of a gene is transcribed into nucleotide sequence of an RNA molecule and then, in most cases, translated into the amino acid sequence of a protein
83
Q

How is the complex task of packaging DNA accomplished?

A
  • by specialized proteins that bind to and fold the DNA
  • this generates a series of coils and loops that provide increasingly higher levels of organization and prevent DNA from getting tangled
  • DNA is folded in a way that allows it to remain accessible to all of the enzymes and other proteins that replicate and repair it and cause expression of its genes

BIO130 (1 decks)

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