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MMBIO 240 > Chapter 3 > Flashcards

Chapter 3 Flashcards

1
Q

What are the two main differences between DNA and RNA?

A
  • RNA has OH on 2’ Carbon. DNA just has H.
  • RNA replaces T with U
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2
Q

Which bases pair with which bases? Which are purines and which are pyrimidines?

A

DNA:
A-T
C-G

RNA:
A-U
C-G

Purines: two rings
G, A (General Authorities:)

Pyrimidines: one ring
C, U, T

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3
Q

What is a Nucleoside?

A

Base + Sugar (deoxyribose in DNA, ribose in RNA)

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4
Q

What is a Nucleotide?

A

Base + Sugar + Phosphate

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5
Q

How are nucleotides connected in a strand? What is the 5’ or 3’ end of the strand and what do 5’ and 3’ refer to on the molecule?

A

PO4 of one nucleotide is bound to the 3’ carbon on sugar of another.
THE PO4 OF ALL NUCLEOTIDES COMES ALREADY ATTATCHED TO 5’ C.

(During DNA synthesis and replication, the DNA polymerase can only add 5’ nucleotides to the 3’ end of a growing DNA strand)

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6
Q

What are the 5 necessary components of an amino acid?

A
  • Central Carbon
    (C)
  • Amino Group
    (NH2)
  • Carboxyl Group
    (COOH)
  • R Group
    (VARIES)
  • Hydrogen
    (H)
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7
Q

How is the R group determined in the creation of amino acids?

A

3 bases of DNA called a ‘codon’ codes for a specific R group in each amino acid

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8
Q

What are Histones? Why are they important?

A

Histone proteins provide double-stranded DNA with something to wind around (allows parts of the chromosome to “close” and “open”)

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9
Q

What is a Nucleosome?

A

The basic structural unit of Chromatin made up of a coil of DNA wrapped around a histone core.

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10
Q

What is Chromatin?

A

A huge rope-like fiber composed of tons of nucleosomes

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11
Q

What is a condensed chromosome?

A

A highly compacted molecule of DNA

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12
Q

Define and diagram the cell cycle including the following stages: G0, G1, S, G2 and M.

A

INTERPHASE
G0 “Resting” Phase:
- the cell is neither dividing nor preparing for cell division

G1 “Growth” Phase:
- cellular contents (excluding chromosomes) are duplicated
- mRNA & protein are synthesized in preparation for DNA synthesis

S “Replication” Phase:
- each of the 46 chromosomes is duplicated (DNA Replication)

G2 “Check” Phase:
- the cell double-checks the duplicated chromosomes for errors
- makes needed repairs

CELL DIVISION
M “Mitosis” Phase:
- one parent cell physically divides into two daughter cells (cytokinesis)

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13
Q

In what stages is DNA condensed (into chromatin) as chromosomes and in what stages is it not?

A

DNA is condensed as chromosomes during Cell Division / Mitosis (specifically beginning with prophase and ending with telophase). They are not condensed during Interphase (G0, G1, S, G2).

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14
Q

What is happening between G1 and G2 phases of the cell cycle?

A

A ton of Protein Synthesis and DNA replication!

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15
Q

What is Epigenetics?

A

The study of how gene EXPRESSION varies in different conditions

(ex: Why do all of the different types of cells in our body look and function differently even though every cell has THE SAME DNA?)

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16
Q

What are the 3 big areas of research having to do with DNA MANAGEMENT within Epigenetics?

(What are 3 different ways that can alter gene expression?)

A

1) Histone Location
(chemical changes affecting gene expression)

2) DNA Modification
(methylation of certain bases)

3) MicroRNAs
(inhibiting protein production)

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17
Q

How does DNA Methylation affect histones? How does it affect genes?

A

Keeps DNA wound up tightly around histones. Methylation turns genes off. Demethylation turns them on!

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18
Q

How can you turn off genes and keep them off?

A

DNA Methylation (altering chemical structure of DNA bases)

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19
Q

Which nucleotides can be methylated? What is added and what is replaced during methylation? What is the consequence of methylated DNA in eukaryotes?

A

Cytosine (C) and Adenine (A) can be methylated.

CH₃ (methyl) is attached to the Nitrogen atom of the base, replacing one of the Hydrogen atoms.

DNA METHYLATION IS CRUTIAL TO GENE EXPRESSION, X CHROMOSOME INACTIVATION, CELLULAR DIFFERENTIATION, AND RESPONSE TO ENVIRONMENTAL FACTORS.

20
Q

What is Inosine? How can uridine be modified?

A

Inosine is a nucleoside that is derived from the deamination (removal of an amino group) of one of the nucleosides.

Uridine can be modified by adding CH3 to the 2’ O (OH -> OCH3)

21
Q

What are five different types of chemical modifications possible on R groups of proteins?

A
  1. Phosphorylation
  2. Acetylation
  3. Ubiquitination
  4. Methylation
  5. Glycosylation
22
Q

Why would we want to modify R groups?

A

Because when the protein folds, we can change how it interacts with other molecules.

23
Q

Periods on periodic table tell us…

A

The number of electron shells

24
Q

Groups on periodic table tell us…

A

The number of valence electrons

25
Q

Families on the periodic table tell us…

A

The chemical behavior of certain elements

26
Q

What is the difference between a negative and positive ion in an ionic bond?

A

Negative ion: gained electron(s)

Positive ion: lost electron(s)

27
Q

What type of ions would elements in groups 1 and 7 tend to form?

A

Elements in group 1 tend to become positive ions.

Elements in group 7 tend to become negative ions.

28
Q

What is the strongest bond (in this biology class)?

A

COVALENT (sharing of electrons)

29
Q

Can you always predict covalent and ionic bonds? How?

A

Covalent: Yes (Lewis dot structures)

Ionic: Not always (BUT we can try with the periodic table)

30
Q

What has to happen before two amino acids create a covalent peptide bond between each other?

A

H2O has to be created from one H of the carboxyl group of one amino acid and one H of the amino group of other amino acid

31
Q

What is resonance? What is one example of resonance in DNA?

A

The movement of electrons within a molecule (changing covalent bond location)

ex: PO4. P has 5 valence electrons but not enough space for the 5 bonds (4 single and 1 double), so the electrons are forced to keep moving!

32
Q

How does the dipole moment occur in a water molecule? (negative on O and positive on H)

A

The electrons are constantly flowing between atoms, creating split-second moments of polarity. Because Oxygen is more electronegative, the electrons will want to move away from Hydrogen and close to Oxygen’s nucleus.

33
Q

What is an H-bond? What elements tend to create H bonds with Hydrogen?

A

Hydrogen Bond: A hydrogen atom covalently bonded to a highly electronegative atom serves as the hydrogen donor. Common hydrogen bond donors include hydrogen atoms bonded to oxygen (O-H), nitrogen (N-H), and fluorine (F-H)

  • MOLECULES MUST BE POLAR (partial positive and partial negative charges)
34
Q

How does a hydrogen bond between water molecules work?

A

Partial positive of H on one molecule attracts partial negative of O on another

35
Q

What is necessary to have in a polar molecule?

A

Difference in electronegativity between .5 -> 2.1

  • HYDROGEN! in most cases hydrogen is one of the only elements that can create this electronegativity difference (H-O bonds in water = 1.4)
36
Q

What makes a molecule hydrophilic?

A

A molecule is hydrophilic if it is:
- polar
- an ion
- can mix with water
- if H-bond can occur

37
Q

What do Van Der Waal’s forces have to do with dipole moments?

A

Everything! Van Der Waal’s forces are simply attractions between two atoms that are close enough experience dipole moments

(the wimpiest of all these interactions!)

38
Q

What determines the folding and shape of RNA strands?

A

The sequence of bases along the RNA strand ultimately determines how it will fold.

39
Q

What is the difference between a stem and a loop of folded RNA?

A

Stem: RNA IMITATING DNA (forming Hydrogen bonds between base pairs and creating a more stable double-stranded structure)

Loop (a.k.a. ‘hairpin loop’ or ‘bulge’): A region with unpaired nucleotides that often create “SEQUENCE MOTIFS”–enabling the RNA to interact with other molecules

40
Q

What is one important factor in PROTEIN folding?

A

Whether the R groups are hydrophilic or hydrophobic (hydrophilic R groups will move inside the protein and hydrophobic R groups will remain on the outside in order to interact with water)

41
Q

What happens when ATP hangs around water?

A

ATP + H2O -> ADP + P

42
Q

About how many ATP molecules are in each cell of our bodies?

A

1 BILLION
(and each ATP molecule only lasts about 2 seconds!!!)

43
Q

How can you get a non-spontaneous reaction to occur?

A

A non-spontaneous reaction requires an external agent like heat or light or energy of some sort to make the reaction start.

44
Q

What is the equation for finding Ph?

A

-log (concentration (M))

45
Q

What is ATP, what is its biological function, and how does it fulfill this function?

A

Adenosine triphosphate is a nucleotide that provides energy to drive and support many processes in living cells. It provides energy through the breaking of bonds.

46
Q

What are Van der Waals forces?

A

Distant-dependent interactions between atoms or molecules, including:
- Weak London Dispersion Forces
- Stronger Dipole-Dipole Forces

  • NO CHEMICAL ELECTRONIC BOND!

MMBIO 240 (15 decks)

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