Bio 140 Test 1 Doyle

Steps of RNA splicing

1) A site within the intron attacks the 5' splice site 2) The cleaved 5' splice site attacks 3' splice site 3) Lariat breaks down, spliced exons are adjacent

Why is Carbon atom so versatile?

1) It has 4 unpaired electrons, so it has 4 total potential bonding sites 2) Wide variety of molecular structures

Scientific Theory

1) Observations 2) Hypothesis 3) Predictions 4) Experiment (if results are not consistent, go to 2) 5) Theory

Van der Waals forces:

1) important in protein-protein interactions 2) weak attractive force that increases up to a distance 3) due to transient asymmetries in electron distribution

H+ concentration calculation:

10^(-pH)

Energy shells:

1st shell: 1 orbital, 2 2nd shell: 4 orbital, 8

Adenine (A) and Thymine (T) are held together by..

2 hydrogen bonds

If (A) is 30%, what is the % of C?

20% %A=%T %G=%C

Guanine (G) and Cytosine (C) are held together by..

3 hydrogen bonds

Components of nucleotides:

5 carbon sugar nitrogen containing base one or more phosphate groups

As RNA travels down DNA, in what direction is an RNA transcript synthesized?

5' to 3'

What must be present at at the promoter and enhancers of a gene for transcription to occur in eukaryotes ?

6+ General transcription factors bind to promoter Transcriptional activator proteins bind to enhancers

The packaging ratio of DNA to Nucleosome is __:__

7:1

What is the relationship between telomeres and cancer?

90% of cancers are associated with high levels of active telomerase enzyme

What nucleotides does the base of RNA contain?

Adenine (A) Cytosine (C) Uracil (U) Guanine (G)

Which 2 of the 5 bases are Purines?

Adenine (A) and Guanine (G)

Stanley Millers experiment resulted in what findings?

Amino acids, Formaldehyde and Hydrogen Cyanide were found, which are building blocks to build macromolecules!

Describe the initial process of DNA transcription in detail

As a region of the DNA duplex unwinds, one strand is used as a template for the synthesis of an RNA transcript that is complementary in sequence to the template according to the base-pairing rules, except using U in place of T

Eukaryotic Chromosomes

Associated w/ proteins Folded and packed into compact structure DNA and proteins together

Describe the RNA-world hypothesis

Because RNA has properties of both DNA (information storage) and proteins (enzymes), many scientists think that RNA was the original information-storage molecule in the earliest forms of life on Earth

___________________ + ___________________ = Nucleosomes

DNA + Histomes

What is the difference between the 5' end of DNA and RNA

DNA is usually a monophosphate while RNA is usually a triphosphate

When calculating difference in [H+]

Divide higher [H+]/lower [H+]

1st law of Thermodynamics

Energy can never be created or destroyed only changed

Introns vs Exons

Exons contain code and are spliced together Introns are noncoding regions that are removed

(T/F) You can predict electronegativities solely based on place on periodic table

FALSE

Unique properties of Water:

Freezes: highly ordered, open, hexagonal structure Many Hydrogen bonds: able to resist temperature change High Boiling temperature: doesn't evaporate as easily

Sequence of nucleotides determines order of amino acids. The order of amino acids determines the 3-D structure. The 3-D structure determines the function of a protein.

KNOW THIS

Non-polar covalent bond: Polar covalent bond: Ionic bond:

Non-polar covalent bond: equal share of electrons Polar covalent bond: unequal share of electrons Ionic bond: complete transfer of 1 or more valence

Hydrogen bonds and Dispersion forces are made up of (full/partial) charges

Partial (+) and (-) charges

Purines have ______ rings while Pyrimidines have ______ rings

Purines: 2 Pyrimidines: 1

What do mediator complex proteins recruit to the site of a promoter?

RNA polymerase complex

If RNA polymerase is properly matched with bases in the template DNA strand, what occurs next?

RNA polymerase orients the oxygen from the hydroxyl group at the 3' end of the growing strand into the innermost phosphate of the incoming ribonucleoside, competing for the covalent end... the polymerization releases a pyrophosphate which is cleaved

The sugar in RNA is ______________ while the sugar in DNA is ________________.

RNA: ribose DNA: deoxyribose

RNA is (single/double) stranded, while DNA is (single/double) stranded.

RNA: single stranded DNA: double stranded

What are telomeres?

Repeated sequences at the tips Required for complete replication of chromosome Protective caps prevent chromosome fusion

DNA vs. RNA structure

Ribose has a hydroxyl group, where deoxyribose has a hydrogen Uracil has a hydrogen where thymine has a methyl group

Histones:

Rich in positively charged amino acids Enable them to form ionic bonds with the (-) charged sugar-phosphate backbone of the DNA 5 classes

What is a nucleotide?

Sugar + Base + Phosphate (or a nucleoside with 1+ phosphate groups)

What is the relationship between telomeres and aging?

Telomere length decreases with age as telomerase levels decline. Addition of telomerase can increase lifespan

What is a lariat and what occurs to it during RNA splicing?

The 5' end of an intron is cleaved onto itself, forming a loop. The 5' end then attacks and cleaves the 3' end from the transcript, and it breaks back into nucleotides

Primary Transcript

The RNA transcript that comes off the template DNA strand

2nd law of Thermodynamics

The degree of disorder in the universe tends to increase

Result of Splicing

The exons are connected and the lariat (made of introns) is quickly broken down into nucleotides

What happens to hydrophobic forces in water?

They are forced into aggregates This minimizes exposure to polar surroundings This decreases entropy of the system

Which 3 of the 5 bases are Pyrimidines?

Thymine (T), Cytosine (C) and Uracil (U)

Summary of DNA

Two chains, right handed double helix Anti-Parallel (5'-3') (3'-5') Sugar-Phosphate backbone Bases, planar, stacked, provide stability Hydrogen bonding Pyrimidine paired with purine Complemenary Major groove, minor groove One turn every 10 residues

Are telomeres affected by stress?

YES, results in shorter telomeres (leads to cell death)

Non-polar covalent bond

a covalent bond between atoms that have the same electronegativity

The reason why bonds form:

atoms are most stable when shells are filled

Isotopes:

atoms of the same element that differ in the number of neutrons in the nucleus

3 domains of life today:

bacteria, archaea, eukarya

What did Erwin Chargaff discover about DNA?

base ratios varied from molecule to molecule, but A=T and C=G always!

DNA and proteins together are called..

chromatin

As simple compounds are combined into more complex molecules the entropy inside of the cell __________, which requires ______________

decreases, energy

The sugar in DNA is _____________

deoxyribose

Valence electrons

electrons in the outermost shell

What is the charge of Ionic bonds?

full (+) and full (-)

__________ is a byproduct of converting energy

heat

what did Oswald Avery, Colin MacLeod, and Jaclyn McCarty discover in 1944?

it is DNA which can transform nonvirulent bacteria into virulent bacteria DNA is the HEREDITARY MOLECULE

Water is more stable interacting with ___________ than other non-polar molecules

itself!

Griffiths Experiment What did he conclude?

molecules can transfer information from one organism to the next

Isomers

molecules that have the same chemical formula but different structures

Model of deep sea vents creating polymers:

monomers + minerals >(heat)> polymers

Biologically relevant electronegative atoms are ___________ and _______________

nitrogen and oxygen

Adenine, Guanine, Thymine and Cytosine are all ...

nitrogenous bases

Put these in order of relative size (small to large): chromatin, nucleotide, DNA, chromosome

nucleotide, DNA, chromatin, chromosome

Once a terminator has signaled the end of transcription of DNA into RNA, what will be at either end of the RNA and what is the benefit of this

one end will have the 5' cap and one end will have the poly-A tail, protecting the RNA from degradation

How many atoms make up an element?

only 1 atom

What element is the most abundant in human cells?

oxygen

in DNA and RNA, nucleotides are connected by ___________ bonds which form a __________ group in one nucleotide, ___________ bonded to a __________ unit of another nucleotide

phosphodiester bond; phosphate group; covalently; sugar

Proteins, Nucleic acid and Sugars are all ____________________, while lipids are NOT

polymers

Proteins are _________ made up of ____________

polymers, monomers

Transcription begins at a ___________ sequence and ends at a ___________ sequence.

promoter, terminator

Electronegativity:

property of an atom that represents the attractive force the nucleus exerts on its electrons

pH expresses _____________________ in a solution

proton concentration

Atomic Mass =

protons + neutrons

The sugar in RNA is _____________

ribose

RNA's have __________ structure

tertiary

Gene definition:

the DNA sequence that corresponds to a specific protein product

What is the '5 cap and why is it necessary in a primary transcript?

the added special nucleotide on to the 5' end of a primary transcript, necessary for recognition by ribosomes

Describe polyadenylation (poly-A tail)

the addition of a string of about 250 consecutive A-bearing ribonucleotides to the 3′ end on mRNA

What primary transcript modification is essential for ribosomal recognition?

the addition of the 5' cap

Peptide bond:

the carbon atom in the carboxyl group of one amino acid is joined to the nitrogen atom in the amino group of the next the combined C-N bond creates a water molecule

What creates surface tension in water molecules?

the cohesive property that water has, w/ many hydrogen bonds (strength in numbers)

Proteins

the key structural and functional molecules that do the work of the cell

RNA Splicing definition-

the process of intron removal

What is a centromere?

the relative center of a chromosome which allows a copy of each duplicated chromosome to go to each daughter cell in mitosis (cell division)

How are telomeres made?

the telomerase enzyme adds sequences to the end of chromosomes

why aren't viruses living organisms?

they cannot harness energy from the environment and therefore cannot read or use their genetic material or regulate passage of substances across their protein coats; they need a cell

Describe the process of transcriptional initiation

transcriptional activator proteins bind to enhancers of promoters, and recruit a mediator complex. The mediator complex then recruits a RNA polymerase complex known as Pol II, which initiates transcription

In prokaryotes, cells without nucleus', ___________ and ____________ are coupled (done at same time)

translation and transcription

Polar covalent bond

unequal sharing of electrons

Hydrogen bond:

weak "attraction" between electronegative atom and a hydrogen bonded to an electronegative atom

Covalent bond:

when 2 atoms share a pair of electrons

Ionic Bond:

when 2 ions are not covalently bound, but because opposite charges attract