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Bio Chp 1 Flashcards

To learn the first chapter of Bio notes (79 cards)

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1
Q

What is the definition of biology generally and briefly?

A

It is the natural science that studies life, organisms including their origin, growth, reproduction, evolution, function, structure, distribution, and taxonomy.

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2
Q

What are five of the fundamental axioms of Biology that involve the concept of evolution?

A

(1) Evolution is the process by which organisms inherit traits and new species are formed.
(2) Genes are the fundamental unit of heredity.

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3
Q

What is the fundamental axiom of Biology as related to cell theory?

A

That, in fact, cells are the fundamental units of life. There is no more basic thing that could be said to be living.

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4
Q

What are the fundamental axioms of biology as related to thermodynamics?

A

(1) An organism regulates its internal environment so as to maintain a stable condition– so called homeostasis.
(2) Living organisms consume and transform energy.

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5
Q

Who discovered the cell? And in what year? What did he examine?

A

Robert Hooke. 1665. Thin slices of cork.

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6
Q

Who was the first to observe a live cell? In what year? What did he examine?

A

Antonie van Leeuwenhoek. 1674. An algae- spirogyra. Bonus: originally named animalcules.

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7
Q

Cell Theory has numerous axioms or generally accepted truths as its foundations. Varying these may be parsed into very roughly nine statements. Can you discuss these?

A

(1) The cell is the fundamental unit of structure and function in all living organisms.
(2) All known living things are made up of one or more cells.
(3) Some organisms are made up of single cells and are called unicellular.
(4) Some organisms are multicellular.
(5) The activity of any organisms depends on the sum of the activities of its independent cells.
(6) All cells arise from pre-existing cells via division.
(7) Energy flow– aka metabolism and biochemistry occurs within cells.
(8) Cells contain hereditary information (genes) which transfer from cell to cell during division.
(9) All cells are of very nearly the same chemical composition when comparing same or similar species.

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8
Q

There are two major subcategories of cells. What are they? What’s the difference?

A

(1) There are prokaryotes. These lack a nucleus, but, ofc, they have circular DNA. They lack most membrane-bound organelles. But they have ribosomes.
(2) Eurkaryotes. These have a membrane-bound organelle called the nucleus. And this contains the genetic info. They also have numerous membrane-bound organelles. They also have organized DNA into chromosomes.

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9
Q

What are the two domains of prokaryotes?

A

Bacteria and Archea.

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10
Q

What are some examples of membrane-bound organelles that you would find in eukaryotes but not in prokaryotes?

A

Mitochondria, chloroplasts, lyosomes, rough and smooth endoplasmic reticulum, vacuol.es

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11
Q

What is the process by which evolution manages the distribution of life?

A

Survival of the fitness aka natural selection. Organisms that are fit survive while unfit organisms die off or are expressed less and less in the population. Fitness is defined always relative to the environment and is variable.

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12
Q

Who was the co-discoverer of evolution? What was his contribution?

A

Alfred Russel Wallace. He researched and experimented with the concept of evolution.

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13
Q

When did Darwin discover evolution?

A

Origin of the Species was published in 1859, so we can use this as a rough marker in time. There was consensus but not broad consensus until approximately 1930s-1950s in the scientific and general communities of evolution. That latter time period saw the so-called modern-synthesis of evolution.

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14
Q

What is genetic drift?

A

Genetric drift is CHANCE events eliminating or changing the frequency of ALLELES in a population.

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15
Q

What is an allele?

A

An allele is a number of alternative forms for the same gene– or genetic locus.

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16
Q

For what kinds of populations is genetic drift important? Why?

A

Genetic drift is more important to small populations because the likelihood of a random change in all or in a significant number of individuals in the population is higher. Thereby, the traits of the future generation may more easily be influenced.

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17
Q

What typical aspect of evolution does genetic drift lack?

A

Changes caused by genetic drift are not necessary adaptive. There is no adaptive pressure or natural selection. They are aimless.

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18
Q

For what two types of events is genetic drift common?

A

Genetic bottlenecks. And founder events.

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19
Q

What is a founder event?

A

This is when a new population is started by a small number of individuals from a much larger population. As a result, the genetic diversity may be significantly reduced. Think 10 humans start a colony on Mars. This may be one mechanism of speciation.

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20
Q

What is a genetic bottleneck?

A

A founder event is a type of genetic bottleneck. A genetic bottleneck is a sudden reduction in the genetic diversity of a population. This may occur due to natural disaster when there is the sudden death of a large portion of the population. As a result, only the genes of the survivors may be passed on influencing future generations and alternating the frequency distribution of alleles.

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21
Q

What is the primary unit of inheritance?

A

Gene

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22
Q

What is the term for how a gene influences the form and function of an organism?

A

Phenotype

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23
Q

What is the term for the genetic information contained with a gene, the complete assemblage thereof?

A

genotype

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24
Q

Roughly speaking, what are the three structural components of a gene?

A

exon-intro-exon

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25
What is homeostasis?
The ability of an open system-- in this case an organism-- to maintain stable conditions within its internal environment. For example, humans maintaining a stable body temp of 38.6 C.
26
Is the homeostasis in living organisms a dynamic or static equilibrium?
It is a dynamic equilibrium. A number in interrelated regulatory mechanisms must interact in order to maintain an internal environment that is stable but not at a typical thermodynamic (or static) equilibrium with the environment.
27
How can an organism maintain a dynamic equilibrium?
It must detect and respond to perturbations
28
What is the typical feedback of an organism in response to a perturbation? Give an example in regards to hypoxia.
An organism generally responds with negative feedback. Example: If there is hypoxia in the circulating blood. There's a receptor for the heme protein. It gets converted to the deoxyconformation. This change is transmitted to the Kidney, which responds by producing erythropoietin, which in turn interacts with the bone marrow to stimulate production of RBCs. Thereby allowing for greater absorption of O2.
29
What are nucleic acids?
They are macromolecules composed of chains of monomeric nucleotides
30
What is a monomer?
This is a molecule that may bind chemically to another molecule to form polymers.
31
What are nucleotides?
These are the compounds: Adenine, Thymine, Guanine, Cytosine.
32
What are the two categories of nucleotides?
Purines and pyrimidine.
33
What are the three component structures of a nucleotide?
A purine or pyrimidine nucleobase. A pentose sugar. And a phosphate group.
34
What is the different between a purine and a pyrimidine nucleobase?
The purines have two ring structures whereas the pyrimidines have a single ring structure.
35
What are the four nucleotide building blocks of DNA?
adenine, guanine, cytsoine, thymine
36
Which ones of the nucleotide building blocks of DNA are purines?
Adenine and Guanine
37
Which ones of the nucleotide building blocks of DNA are pyrimidines
Cytosine and Thymine
38
Roughly draw the structure of a Purine.
See ref.
39
Roughly draw the structure of a Pyrimidine
See ref.
40
What is the/a difference between DNA and RNA in terms of chemical structure?
On the 2nd carbon of the pentose sugar, DNA is missing an oxygen as compared to RNA. RNA has the hydroxyl group attached to the pentose ring. So DNA is 2-Deoxy-D-Ribose. And RNA is D-Ribose.
41
What are the rules of base pairing?
G-C, A-T. So a Purine always matches with a Pyrimidine.
42
What is the radius of the DNA Helix?
1 nm
43
What is the length along the central axis of a DNA helix that it takes for one full twist?
3.4 nm
44
What are the chemical bonds that line the monomers of nucleotides together to form single strands of DNA?
The phosphate group on any nucleotide lends an oxygen to the hydroxyl group on the 3' carbon of the ribose in the next nucleotide. The nucleotides may be strung together one after the other in such a fashion. Sketch schematically
45
What type of interaction holds together the nucleobases in two stranges of DNA so that they form their helical shape?
Hydrogen bonding between the base pairs glues the two strands together.
46
What is the convention for sequencing the nucleotides of a strand of DNA?
Generally, one starts at the 5' end as the left-terminus and then writes the sequence until the 3' end as the right-terminus. Proceeding in the opposite direction is considered the complementary strand.
47
What nucleic acid is different between DNA and RNA?
RNA has Uracil instead of Thymine. Another pyrimidine.
48
What is chemically the methylation of DNA?
For animals and plants, this means cytosines are methylated. In bacteria, adenine can also be methylated.
49
What does DNA methylation do?
It stably alters the expression of genes on a strand of DNA. At present, it appears responsible for the differentiation of cells from stem cells. It also appears to be a unidirectional and irreversible process thereby preventing a cell from reverting to a stem cell.
50
At what sites in DNA does methylation in mammals typically occur?
It typically occurs at "CpG" sites. There is not to be confused with base pairing of C and G. Rather on a single strand of DNA where C is linked via a phosphate to a G, there on the C methylation can occur.
51
Does methylation play a role in cancer? How?
Yes, methylation can play a role in cancer when normally unmethylated regions of DNA become highly methylated. This alternation can be passed onto daughter cells and result in altered or silenced expression of genes.
52
What can RNA strands do that DNA typically does not?
RNA strands tend to form complicated three dimensional structures that DNA does not since it is generally bound tightly into its repetitive and restricted double helical structure.
53
What molecules help make RNA? What is the name of this process?
RNA polymerases are catalysts/enzymes that help copy DNA or RNA into more RNA through a process known as transcription.
54
What is a protein?
A biochemical compound consisting of one or more polypetides typically folded into globular or fibrous form. The form generally corresponds to biological function.
55
What is a polypetide?
1. It's a polymer. 2. It's a polymer consisting of amino acids. 3. The amino acids are linked together by bonds between the carboxyl and amino groups of adjacent amino acids.
56
How are sequences of amino acids encoded?
The amino acid sequence is encoded by the sequence of base pairs in a gene. DNA converts into RNA via TRANSCRIPTION. RNA converts into a protein via TRANSLATION.
57
What is the basic structure of an amino acid?
It consists of an amine gruop, a carboxylic acid group, and a side-chain, which varies between different amino acids. Sketch
58
How many amino acids are there?
20
59
What are the non-polar amino acids?
Glycine, Aladine, Valine, Leucine, Isoleucine, Proline
60
What are the Polar, uncharged amino acids?
Serine, Threonine, Cysteine, Methionine, Aspargine, Glutamine
61
What amino acids have aromatic side chains?
Phenylalanine, Tyrosine, Tryptophan
62
What amino acids have positively charged R groups?
Lysine, Arginine, Histidine
63
What amino acids have negatively charged R groups?
Aspartate, Glutamate
64
How is the peptide bond formed between amino acids? What type of reaction is it?
First, it's a condensation reaction, which means water is left over at the bonds are formed. Essentially, one hydrogen of the amino group and the hydroxyl group of the carboxylic acid combine to form water and leave a C-N bond to link the amino acids.
65
Sketch peptide bond formation.
See ref.
66
What is the primary structure of proteins?
This refers to the sequence of amino acids that forms a protein. It's chemical constituents.
67
What is the convention for the primary structure of proteins?
By convention, the primary structure of a protein is reported starting with the N-terminus and ending with the C-terminus. This means that the amino acid with the amine group sticking out is the first reported amino acid when reading the sequence left to right.
68
What are the three types of secondary structure for a protein?
Alpha helix, beta sheet, and random coil
69
What is the secondary structure "alpha helix" in regards to proteins? What forces are dictating this structure?
Alpha helixes are formed by hyodrgen bonding between carboxyl and amine groups of the amino acids with the side chains jutting out from the helix. The hydrogen bond typically happens between the amine group of a given amino acid and the carboxyl group of the amino acid four earlier in the sequence. This is the most common secondary structure.
70
What is the secondary structure of "beta sheets" in regards to proteins? What forces are dictating this structure?
Hydrogen bonding is again responsible for beta sheets. The side chains are alternating pointing straight up and down. And the polypetide is pleated. Many polypetides in this configuration form a pleated sheet.
71
What is the secondary structure of "random coil"?
This is actually an umbrella term of all the secondary structures of proteins that are not either alpha helix or beta sheet or where there is an absence of any regularity in structure.
72
What is the difference between the secondary and tertiary structure of proteins?
The tertiary structure of proteins is generally an interaction between the side groups of the polypetides. It also tends to occur between amino acids that are far apart in the primary structure. So the interactions only occur after some sort of folding process. Thus, the tertiary structure tends to be a complicated three dimensional conformation. The physical forces involved are hydrogen bonding again, ionic bonding, non-polar interactions (Van der Waals forces), and also so-called disulfide bonds (sometimes called bridges). Uniquely the disulfide bonds are covalent bonds as opposed to the other interactions forming tertiary structure.
73
What is the difference between tertiary structure and quaternary structure? Why the distinction?
Firstly, in quaternary structure there are TWO or MORE polypetides linked together. They form the actually sum total of the protein. All types of interactions occur. These are the final form bioactive proteins like insulin, collagen, and hemoglobin.
74
What is a conjugated protein?
This is in reference to the quarternary structure of a protein in where it has a so-called prosthetic group, which is a non-polypetide structure. For example, in hemoglobin, the four polypetides are linked to a heme group which is not made up of amino acids.
75
What is an example of a conjugated protein and its quaternary structure?
Hemoglobin has four polypetides linked to a heme group, which is not made of amino acids.
76
There are at least nine functions of the final form quaternary structured proteins. List them.
(1) Enzymes (2) Transport proteins (3) Membrane Proteins (4) Immunologically active proteins (5) Proteins used for motility (6) Regulatory proteins (7) Receptor Proteins (8) Storage Proteins (9) Structural proteins
77
What are some of the classes of molecules that would be considered lipids?
(1) Fats (2) Waxes (3) Sterols (4) Fat-soluble vitamins (A, D, E, K), mono/di-glycerides, phospholipids, etc.
78
What are the three main functions of lipids?
(1) energy storage (2) membrane structure (3) signaling molecules
79
Broadly, how may we define lipids?
They are molecules. Not terribly large, which is vague, but importantly they are either hydrophobic or amphiphilic.

Biomechanics (5 decks)

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