BIO 130 Midterm

True or false

Single-celled organisms refer to prokaryotic cells.

False; eukaryotes can be single-celled too

3 major domains of life

Eukaryotes, bacteria, and archaea

3 shapes of bacterial cells

Spherical, rod-shaped, spiral

Archaea resemble ___ in outward appearance but genomes more closely related to ___

bacteria; eukaryotes

Differences between prokaryotic and eukaryotic cells

1. Prokaryotic does not have nucleolus

2. Eukaryotes are mainly multiple-celled

3. Prokaryotes do not have membrane'-bound organelles

4. Prokaryotes have less DNA than eukaryotes

What does the entangle-engulf-endogenize model try explain?

hypothesizes that mitochondria was originally free living prokaryotes able to use oxygen and was engulfed by an anaerobic archaeal cell, resulting in endosymbiosis and aerobic eukaryotic cells.

Evidence for endosymbiont hypothesis for origin of mitochondria and chloroplasts

1. Both have own genome and similar genetic to modern-day prokaryotes

2. both kept some of their own proteins and DNA synthesis components

3. Both membranes similar to prokaryotes and derived from engulfed bacterial ancestors

Central Dogma of molecular biology

DNA → RNA → Protein

Transcription → translation

what is a nucleotide and what are the three parts:

Nucleotide is a subunit of nucleic acids.

1. pentose sugar (scaffold for base)

2. nitrogenous base

3. Phosphate group (backbone)

The phosphate group attaches to ___ carbon and the nitrogenous base to the ___ carbon

5’; 1’

Difference between pyrimidine and purine, which one is stronger, and why?

Pyrimidines have one right while purines have two, which is why purines are stronger.

Pyrimidine: U, C, T

Purine: A, G

Deoxyribose lost an oxygen on the ___ carbon

2’

Name the following structures:

1. sugar + base + 2P

2. base + sugar + at least 1 P

3. Base + sugar

1. Nucleoside diphosphate

2. Nucleotide

3. Nucleoside

nucleoside __phosphate is a type of nucleotide!

Different Nucleic acid chains:

1. DNA synthesized from ___

2. RNA synthesized from ___

3. Nucleotides linked by ___

1. dNTP

2. NTP

3. phosphodiester bonds

How are phosphodiester bonds formed?

OH on the 3’ of the pentose sugar forms covalent bond with phosphate group, and two phosphate groups are lost due to hydrolyzation.

What holds the DNA double helix together?

hydrogen bonds between bases

Which base pairing is stronger and why?

G-C because they make 3 hydrogen bonds while A-T only make 2

What are the three forces that keep DNA strand together?

1. hydrogen bonds

2. hydrophobic interactions (bases are very hydrophobic)

3. van der Waals attractions

DNA backbone has___ charge

negative

True or false

Heating DNA leads to permanent denaturation to single bonds by breaking hydrogen bonds.

False; renaturation can restore DNA double helices

1. Strands in double helix are ___ and ___ to each other

2. The two ends of DNA are:

3. Separating/rejoining DNA strands is ____ performed by proteins

1. antiparallel; complementary

2. 5’ phosphate group (PO4); 3’ hydroxyl group (OH)

3. reversible process

Amino acid is composed of:

1. alpha carbon

2. carboxyl group

3. Amino group

4. R-group

Why is cysteine AA special?

It can undergo disulphide bonds under oxidation which very strong and holds protein shape

Ribosomes are needed to make peptide bonds by taking ___ from carboxyl group and ___ from the amino group to form a ___ molecule. This reaction is called ___.

OH; H; water; condensation

In the bond that forms after condensation, the C is called ___ carbon and the N is called the ___ nitrogen

carbonyl; amide

True or false

The backbone of a protein consists of all the protein’s atoms except for the side chains (R-chains)

True

Alpha folding involves ___ n forms hydrogen bonds with n+__

Residue; 4

Which two atoms form hydrogen bonds in alpha helices?

Oxygen from carbonyl (C=O) with H from amide group (N-H)

Alpha helix vs. Double helix

1. single strand vs double strand

2. side chains face outward vs base pairs face inward

3. R groups do not hold structure together vs. base pairs hold structure together

4. N and C ends vs. 5’ and 3’ ends

What stabilizes alpha helix?

hydrogen bonds between carbonyl oxygen and amide hydrogen

Beta sheet is nearly ___ due to H-bonding between carbonyl oxygen and amide nitrogen in ___ strands

linear; neighboring

two types of beta sheet

1. Anti-parallel: adjacent strands run in opposite directions

2. Parallel: (N-terminus to C-terminus)

What is a coiled coil

a type of alpha helix called amphipathic helix (a chemical compound containing both polar and nonpolar portions in its structure)

The tertiary structure of a protein is held together by 3 forces:

1. hydrophobic

2. non-covalent bonds

3. covalent di-sulfide bonds

True or false

Proteins generally fold into the conformation that is most energetically favourable, and chaperone proteins help make the process more efficient and reliable in living cells

True

What is a protein domain and what level of structure of protein is it found in?

portion of a protein that has its own tertiary structure, often functioning in semi-independent manner; together make overall tertiary structure.

Molecular machines

molecules that move in a mechanical way in response to an external stimuli

True or false

Genome size is correlated with organism size, organism complexity, or number of genes

False; it does not correlate with the listed

Why are some eukaryote genome size so small compred to E coli

Some mitochondrial DNA became nuclear DNA

Human genome has ~___ base pairs per genome, so in one standard cell, a total of ___ chromosomes and ~___ base pairs

3; 46; 6

What percentage of genome is repetitive DNA and how much encode protein?

~50 % and less than 1%

Repeated sequences have:

1. segment duplications

2. simple repeats

3. mobile genetic elements (sequences that sometimes cut themselves out of DNA, sometimes make copy, sometimes paste themselves back in)

What is FISH used for

a diagnostic technique to detect the presence of a specific sequence, relies on antiparallel binding

Chromosomes contains single, long, linear DNA molecule and associated proteins called ___

chromatin which is made of DNA+proteins and is dynamic

Beads on a string

DNA double helix (red line) wraps around proteins (yellow circles) one and two-thirds times; a form of chromatin

Most chromatins are ___ fiber

30nm

Nucleosomes are made up of

core histones + DNA around it + H1

Histones

small proteins rich in lysine and arginine; Positive charge neutralizes negative charge of DNA (helps it bind)

How many linker histones are there and what does it do?

One linker histone (H1)

• Clips the DNA on; acts like a paper clip

• Without H1 it is not enough to stick two nucleosomes together

Nucleosome core particle

core histones + DNA around it (does not include H1)

Sequence-specific clamp proteins and ___ are involved in forming chromatin loops. As cells enter mitosis, ___ replace most cohesins to form double loops of chromatin to generate compact chromosome

cohesins; condensins

Heterochromatin

highly condensed chromatin

Heterochromatic regions of interphase chromosomes are areas where gene expression is ___

suppressed

Euchromatin:

relatively non-condensed chromatin, tend to be expressed

Heterochromatin ←→ Euchromatin

Degree of chromatin condensation; reversible switching between the two

Semiconservative DNA synthesis:

during replication, original double helix unwinds and each serves as separate template

DNA polymerase catalyzes DNA synthesis by using the energy from ___

cutting two phosphates off

characteristics of the sequences where replication origins include:

Easy to open, A-T rich (easier to break because only 2 hydrogen bonds)

Steps in bacterial DNA replication

1. origin of replication

2. binding of initiator proteins

3. unwinding by helicase

4. Binding of single-strand binding protein

5. RNAp primers made by primase

6. DNA polymerase binds to primers and starts adding nucleotides

DNA topoisomerase

Cuts an opening and spins helix to release tension to reduce supercoiling & torsional strain as helicase unwinds DNA

The shortening of the 5’ end of the daughter DNA is a potential problem because of loss of sequence information. Why does this occur?

Primase not good at putting primer right at the end; After primer gets removed there’s a 5’ end and new DNA can’t be added, so information is being lost

Telomerase

it is an enzyme responsible for maintaining the length of telomeres, the protective caps at the ends of chromosomes, by adding DNA repeats to them

Loss of telomeres, which occurs normally during DNA replication, limits the number of rounds of ___

cell division

2 mechanisms for DNA replication proofreading and repair:

1. 3’ to 5’ exonuclease: removes misincorporated nucleotide

2. Strand-directed mismatch repair: a DNA replication error repair process (if proofreading fails)

UV causes ___ dimers, which are lesions formed between adjacent ___

pyrimidine

Two types of genes when transcribed

1. resulting RNA encodes protein

   1. mRNA

2. resulting RNA functions as RNA and may not be translated into protein

   1. tRNA, rRNA

True or false

Both RNA and DNA polymerase require primer

False; RNA polymerase does not need primer

RNAP holoenzyme

RNA polymerase core enzyme + sigma factor

Bacterial transcription cycle:

1. sigma factor binds to RNAP holoenzyme, and finds promoter sequence

2. Localized unwinding of DNA, RNAP clamps down and sigma factor released

3. elongation

4. Termination and release of RNA

Directionality of promotor sequences

Upstream (-) → Downstream (+)

Promoter consensus sequences

shown (-10, -35); where sigma factors bind to

Terminator sequences usually consist of __ and __ , followed by lots of __ and __

G’s; C’s; T’s; A’s

True or false

Initial steps of RNA synthesis are relatively inefficient

True

In prokaryotes, transcription and translation are ___

coupled

a final processed eukaryotic mRNA should have:

1. 5’ cap and poly-A tail for protection

2. All introns are cut out

3. UTRs in leftover exons before and after coding sequences

Types of eukaryotic RNA polymerases:

• RNA polymerase I: does most rRNA genes

• RNA polymerase II: does all protein-coding genes

• RNA polymerase III: does the tRNAs

RNA Pol II has special ___ not found in bacterial or other eukaryotic RNAPs

carboxyl terminal domain (CTD)

Each subunit in RNAP II and prokaryotic has both ___ and ___, but one subunit in RNAP II also has CTD

N-terminus; C-terminus

Eukaryotic vs. bacterial RNA polymerases:

Eukaryotic RNA polymerases require proteins to help position them at the promotor called ___

transcription factors

TATA box

 the sequence TATA (close to that) is highly conserved, found ~30 bp upstream before start site for transcription

In eukaryotic promoters, there will be 1 or more specific sequences called ___ which are recognized by specific ___

elements; general transcription factors

What is TBP

TATA binding protein, a subunit of TFIID

Steps in the initiation of transcription for eukaryotes:

1. TBP of TFIID binds to TATA box

2. Other transcription factors bind

3. RNAP II binds at transcription start site

4. Helicase activity & phosphorylation of C-terminal of RNAP II performed by TFIIH

1. How is RNA polymerase II activated?

2. What is phosphorylated?

1. phosphorylation of the carboxyl terminal domain (tail)

2. Adding phosphate groups on all the S (Ser)

In RNAP II only, the carboxyl terminal domain of the largest subunit has a stretch of 7 amino acids that is repeated multiple times.

Tandem repeats

Eukaryotic mRNA processing 3 steps:

1. addition of 5’ cap

2. removal of introns (splicing)

3. processing and polyadenylation of 3’ tail

5’ pre mRNA cap…

helps protect RNA from exonucleases

how does splisosome protein splice

takes OH off 2’ carbon

Splicing reaction for most eukaryotic pre mRNAs require ___ which are contained in spliceosomes

snRNPs

When splicing complete, ___ added which sits where introns used to be, which helps ___ the spliced mRNA from the nucleus to the cytoplasm

exon junction complex

What is the site of protein synthesis?

the cytosol

tRNA

recognize the codon on the mRNA and bring the proper amino acid

True or false

The amino acid is attached to the 5’ end of tRNA

False; its attached to the 3’ end

True or false

More than 1 tRNa for many amino acids

True

What is a wobble position and where is it?

represents flexible base pairing, enables single tRNA to recognize multiple codons coding for the same amino acid.

Always on the 5’ end of the anticodon and 3’ end of the mRNA

Aminoacyl-tRNA synthetases

Get amino acid and put it on the correct tRNA. Typically 20 different synthases, one for each amino acid.

3 sites on a ribosome and their functions

• A site: aminoacyl site; newly tRNAs bind

• P site: peptidyl site; holds the tRNA that is linked to to growing peptide chain

• E site: exit site; where amino acid leaves

Peptide bond formation is catalyzed by the ___ activity of the rRNA in the large subunit

peptidyl transferase

Two quality checks during translation

First check: EF-Tu (EF1 in euk.) checks aminoacyl tRNA (tRNA with new amino acid)

Second check: correct anticodon-codon base pairing

If base-pairing correct, ___ hydrolyzed & EF-Tu released

GTP