Exam 1 Study Guide

What is the central dogma of information in biology?

DNA → transcription → RNA → translation → protein

What are the two main functions of proteins?

to build structures and perform jobs in the body

what are the major components of the cell?

nucleus, golgi apparatus, mitochondria, plasma membrane, endoplasmic reticulum, ribosome

What are the 5 nitrogenous bases? Which other bases do they base-pair with in both DNA and RNA?

Cytosine, thymine, guanine, uracil, and adenine. C-G, T-A, A-U

Is mRNA + or - sense?

mRNA is a single stranded positive sense strand

what is the + DNA strand?

sense, nontemplate, information, and coding strand

- DNA strand

complementary, antisense, template strand

What is the significance of 3'-->5' in relation to DNA and RNA?

Translation and transcription synthesize in the 5'-->3' direction

what does it mean when we say DNA has an anti-parallel structure?

it has two complimentary strands, one going 5'-->3', and the other going 3'-->5'.

5' and 3' refer to carbon positions on the sugar, and the polymerases add to the 3' OH

Does a chromosome only have one coding strand? Do all the genes "face" the same direction?

No! Either strand can be the coding strand, and genes can run either direction

What direction is the coding strand? 3' to 5' or 5' to 3'? In what direction is the RNA being synthesized?

The coding strand goes 5'-->3', and RNA is synthesized 5'-->3', but the template strand is read 3'-->5'

Replication

DNA-->DNA

Transcription

DNA-->RNA

Translation

RNA-->protein

What is a codon?

In a nucleic acid, a sequence of three adjacent nucleotides that codes for a specific amino acid or a stop signal.

How many pairs make a codon?

Three base pairs make a codon

What are amino acids used to build? How many amino acids are there?

proteins; there are 20 amino acids

What is an R group?

a variable chemical group attached to the central alpha-carbon of an amino acid. It characterizes an amino acid. Side chain that defines function

What are three possible locations of a ribosome in the cell?

1. the ribosome can be over a channel in the membrane, so the protein will be in the lumen of the E.R. and end up inside a vesicle or released outside of the cell.

2. the ribosome can be directly on the membrane of the E.R., so the protein is inserted into the membrane and will end up in the membrane of a vesicle or on the plasma membrane

3. in the cytoplasm

What are the different stages of a the cell cycle?

Go, G1, S, G2, Mitosis/Meiosis

G0

resting phase

G1

cells are diploid, containing two copies of each chromosome. Growth stage, prep for synthesis

S stage

DNA synthesis. Each chromosome is duplicated, and two identical chromosomes remain together as a sister chromatid pair. At the end of the phase, each homologous chromosome exists as a sister chromatid pair, and thus the cell now contains four copies of each chromosome in the form of two sister chromatid pairs

G2 phase

another growth stage, prep for cell division

M phase (mitosis

duplicated chromosomes separate completely and the cell divides into two daughter cells

Why is DNA synthesis referred to as "semi-conservative?"

each daughter duplex has one intact parental strand and one newly synthesized strand

True or false: all of the cells in the body have the same DNA

True!

What is epigenetics?

Different cells express different genes, meaning different situations cause cells to express different genes, often via methylation or histone modification

What are the 3 components of a DNA or RNA nucleotide? Which parts make up the "backbone" of a DNA/RNA strand?

phosphate, sugar, and base

DNA/RNA have a backbone made of sugar and phosphate.

What is the difference between an RNA and DNA nucleotide?

RNA nucleotide has a OH on 2' instead of a H on 2'. Base pairs are also different, and DNA has a deoxyribose sugar while RNA is a ribose sugar. DNA has thymine, while RNA has uracil.

What is the type of bond that holds the two strands of DNA together?

a hydrogen bond, but base stacking (van der waals) contributes most to stability

Why is the C-G pair stronger than an A-T pair?

The C-G pair has three hydrogen bonds, while the A-T pair only has two hydrogen bonds.

What is methylation?

adds a methyl group to the DNA base.

What is amination?

Amination is when an amine group is attached to a DNA base. Uses NH2

Briefly, what is the difference between an ionic and covalent bond?

Ionic bonds are between nonmetals and metals with a large difference in electronegativity, in which one element transfers the electron.

covalent bond is sharing an electron, typically between two nonmetals.

What is an ion?

a charged molecule

What is a valence shell? How many electrons can a valence shell hold?

The outermost shell. 8 electrons

How many covalent bonds can carbon, oxygen, and nitrogen make?

4, 2, 3

What is the difference between a polar and nonpolar molecule?

Polar molecules have a large difference in electronegativity, such that the electrons are shared unequally between the atoms.

Nonpolar molecules have similar electronegativity, thus no dipole moment and are therefore poorly soluble in water.

What is a dipole moment?

when more electrons are clustered around one element than the other.

What is a hydrogen bond ? What kinds of molecules can form them?

a weak electrostatic attraction between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom. Formed by N, F, O.

What are Van der Waals forces? How do base-pairs utilize them in their stacking?

weak intermolecular forces between molecules as a result of each molecule inducing polarization in the other. They are stacked on top of each other with optimal van der waals spacing

What is a phosphodiester bond?

Two ester bonds connected with a phosphate, for DNA backbones

What is the difference between a base, a nucleoside, and a nucleotide?

Base: nitrogen-containing basic compounds

nucleoside: a compound consisting of a purine or pyrimidine base covalently linked to a pentose

nucleotide: a nucleoside phosphorylated at one or more of its pentose hydroxyl groups

What does ATP stand for?

Adenosine triphosphate

What would the molecule be called if adenosine were bound to two phosphate groups?

Adenosine diphosphate

What would the molecule be called if it were bound to one phosphate group?

Adenosine monophosphate

What does NTP mean?

Nucleotide triphosphate

What do dNTP and rNTP mean?

DNA nucleotide triphosphate

RNA nucleotide triphosphate

Which of the nitrogenous bases are purines and which are pyrimidines?

Guanine and Adenine: purine

Thymine, cytosine, uracil: pyrimidines

What are the two products made when ATP is used in the cell? Is this reaction reversible?

When ATP is used in the cell, the two products are ADP and Pi. This reaction is reversible

What is pyrophosphate? If it s removed from ATP, is that reaction reversible? How would you return AMP to ATP?

Pyrophosphate is two phosphates linked together, which is what is produced when AMp is produced from ATP. it is irreversible. It takes ATP reacting with AMP to make two ADP, which then go through multiple enzymatic steps

What does a negative delta G mean for a reaction?

it means the reaction is spontaneous

What is an enzyme?

a biomolecule, either protein or RNA, that catalyzes a specific chemical reaction. It does not affect the equilibrium of the catalyzed reaction; it enhances the rate of the reaction by providing a reaction path with lower activation energy

What are the two laws of thermodynamics

1. energy can never be created or destroyed. -- ATP+H2O--> ADP +Pi+energy

2. all spontaneous processes take place with an increase in disorder, called entropy, of the system. ex: ATP hydrolysis increases entropy because one ATP molecule becomes ADP+Pi.

Protease

a protein that cuts other proteins

What does coupling a reaction mean? How is it used to drive forward unfavorable reactions?

Coupling a reaction means using a spontaneous reaction to drive an unspontaneous reaction, so the energy from the spontaneous reaction drives the unspontaneous reaction

What is DNase?

Enzyme that cuts DNA

how does gel electrophoresis help us differentiate segments of DNA?

DNA fragments move towards positive side according to size. Smaller fragments move faster and bigger fragmetns move more slowly. A band represents DNA of a particular size. DNA has an overall negative charge.

What is the difference between an endonuclease and an exonuclease?

Endonuclease cuts in the middle. an enzyme that hydrolyzes the interior phosphodiester bonds of a nucleic acid; that is, it acts at bonds other than the terminal bonds.

Exonuclease cuts at the end.

restriction endonuclease

cuts at a specific sequence

How do enzymes work?

To make reactions occur, the protein enzyme needs to grab a ligand, form complex PL, which results in a conformational shift

What is a ligand?

any molecule, small or large, that is specifically bound by a protein without altering that bound molecule; for example, a hormone is the ligand for its specific protein receptor.

What is a conformational shift?

protien changes shape to complete a job

Major and minor grooves. Where do DNA-binding proteins typically bind? Are proteins able to "read" DNA sequences?

Major groove: the wider of two grooves that wind around the outside of a DNA double helix.

Minor groove: the narrower of two grooves that wind around the outside of a DNA double helix

DNA-binding proteins typically bind to the major groove, and they read DNA sequences to do so.

Cofactors

positive ions that help the proteins better interact with nucleic acids. an inorganic ion or a coenzyme required enzyme activity

coenzymes

organic cofactor that is required for the action of certain enzymes.

what do cofactors and coenzymes do in relation to enzymes?

They can bind to DNA to protect cells from reactive oxygen species, repair DNA, recombinational DNA repair, DNA cleavage, nucleic acid synthesis

What keeps nucleic acids in the favored state and what can disrupt them?

Van der waals and hydrogen bonds hold things together, while interactions with cofactors disrupt them

What are Chargaff's ratios?

In all cellular DNA, regardless of the species, the amount of A equals the amount of T, and the amount of G equals the amount of C. Proves that A-T, and G-C.

What does it mean to denature or melt DNA? What intermolecular interactions are being disrupted in this process?

Denaturing is disconnecting the strands. Disrupts the hydrogen bonds.

What is the nascent strand? what direction is it formed in?

The new strand formed in DNA synthesis. It is formed in the 5'-->3' direction

What is a palindrome sequence?

when the bases are mirrors of each other so that they can form cruciforms. for example: 3'-GAA~TTC-5' and 5'-CTT~AAG-3'

What is a mirror repeat and how is it different from a palindrome sequence?

a DNA sequence that displays symmetry on a single strand, where a sequence is followed by its reverse on the same strand. In contrast, a palindromic sequence is a double-stranded sequence where the sequence on one strand, read 5'-3', matches the sequence on the complementary strand read 5'-3'.

What are the main stages in both mitosis and meiosis? How do these processes differ?

Prophase, Metaphase, Anaphase, Telophase. Mitosis produces two genetically identical diploid somatic cells for growth and repair in one division cycle. Meiosis produces four genetically unique haploid gametes through two division rounds, reducing the chromosome number by half.

How is DNA packaed/condensed?

DNA is wrapped around histone proteins, which form nucleosomes, or "beads on a string." Nucleosomes then coild and fold into chromatins, which are coiled, and then codensed into chromatids, which are joined together with the centromere.

What are nucleosomes?

In eukaryotes, the structural unit for packaging chromatin, consists of DNA strand wound around a histone core

centromere

attachment point for the mitotic or meiotic spindle

Telomeres

a specialized nucleic acid structure found at the ends of linear eukaryotic chromosomes. ends of the chromosomes. they are protective caps that prevent DNA degradation, shortening, or fusion with neighboring chromosomes

What is a nucleoid region in bacteria? How is different from how eukaryotic chromosomes?

the nuclear zone that contains the chromosome but has no surrounding membrane. Where the DNA is stored, in which it wraps in and out of this tube thing with different holes.

Core proteins

the protein organizing the nucleoid region in bacteria

what is a plasmid?

prokaryotic extrachromosomal DNA

Do mitochondria contain their own DNA?

yes, referred to as mtDNA

Writhe

large loops across entire structure of DNA. the net number of supercoils in a DNA molecule

Twist

# of bases before turn of the helix

Linking number

the number of times one closed circular DNA strand is wound about another; the number of topological links holding the circles together

Prophase

the first stage of mitosis. chromosomes duplicated in S phase begin to condense into visible, X-shaped sister chromatids, and the nuclear envelope breaks down

Metaphase:

the second stage of mitosis. the spindle apparatus directs condensed sister chromatids pairs to align along the metaphase plate

anaphase

the third stage of mitosis. Sister chromatid pairs held together at the centromere separate, and the two homologous chromosomes move toward opposite spindle poles

telophase

the final stage of mitosis, in which the two sets of homologous chromosomes reach opposite spindles poles and begin to decondense. the cell physcially divides in the process of cytokinesis, resulting in two daughter cells

How does the linking number change ahead of and behind DNA polymerase or RNA polymerase during DNA replication or transcription, and where does overwound versus underwound DNA accumulate?

Overwound occurs in front of DNA replication (higher LK#), and underwound occurs afterwards (lower LK#)

What is the difference between positive and negative supercoils

Positive: the over-winding of the DNA double helix in a right-handed direction, increasing the number of times strands wrap around each other

negative: the underwinding of the DNA double helix, where the DNA is twisted in a left-handed direction, reducing the number of helical turns

Function of topoisomerase

to uncoil DNA

Type I topoisomerase

reduces twist to reduce writhe.

they do not use ATP

use a nick and turn helix and ligate.

reduces negative supercoils

Type II topoisomerase

reduce writhe

use ATP

use Double stranded break (DSB)

DNAgyrase, Topo II

introduces negative supercoils

Found in prokaryotes

Where are DNA gyrase found?

prokaryotes

Examples of how to use the "___-dependent___polymerase" format of naming polymerases as well as the shorthand names

DNA---> DNA. DNA dependent DNA polymerase (DNA polymerase)

DNA-->RNA. DNA dependent RNA polymerase (RNA polymerase)

RNA-->DNA. RNA dependent DNA polymerase (for reverse transcription)

What does it mean when bacterial chromosomes are catenated? How is this resolved?

when two or more circular polymeric molecules interlinked by one or more noncovalent topological links, resembling the links of a chain. Resolved through Topo IV doing its thing.

what is the function of reveres transcriptase?

RNA-->DNA; only used in viruses

Why is an RNA primer required during DNA replication, and what role does it play in initiating DNA synthesis?

For the RNA polymerase to latch on, it needs double strands to do its job.