MBB11003

MolCell

What are the 3 classification domains of organisms?

Bacteria, archaea, eukaryotes

What are some cellular characteristics?

Grow and divide, obtain energy from light/chemicals, pass on hereditary information

What organelles do eukaryotic cells contain?

Nucleus, mitochondria, endoplasmic reticulum, golgi, cell membrane, cell wall, lysozymes, peroxisomes, chloroplasts & vacuoles (plants)

What is DNA?

deoxyribonucleic acid is a polymer of nucleotides (A,T,C,G)

What is the central dogma?

DNA-transcription-RNA-translation-protein

What is a protein?

polymer of amino acids

What determines the shape of a protein?

sequence of amino acids

How does protein shape relate to its function?

The shape of a protein allows it to carry out a specific function

What is a polymer?

chain of monomers

What is RNA?

single-stranded nucleic acid polymer that contains the sugar ribose

What are some functions of proteins?

Structural, cell recognition, moving molecules, enzymes

What are microtubules?

hollow structures made up of the protein tubulin (alpha & beta subunits), that maintain a cells shape

What is an enzyme?

Protein that catalyse rates of chemical reactions

Describe the structure of a protein

Long chain of amino acids with varied side groups. Proteins can vary in shape, size, charge & polarity

What is the primary structure of a protein?

sequence of amino acids (residues) in a polypeptide chain

What determines the amino acid sequence?

genes (3 DNA bases code for 1 amino acid)

What bond joins amino acids together?

peptide

What is the function of the N and C terminus?

Mark the beginning and end of the amino acid chain

Can rotation occur around a peptide bond?

No

What is the secondary structure of a protein?

1) Twisting of the alpha helix
2) Beta sheets
3) Hydrogen bonding

What do chaperone proteins do?

Assist in the proper folding of proteins

What do hydrogen bonds between NH and CO group of amino acids provide?

Stability

Describe the structure of an alpha helix.

rod like structure where a tightly coiled backbone forms the inner part of the rod and the side chains extend outward in a helical array. H bonds form between NH and CO groups 4 residues apart.

Describe the structure of a beta plated sheet.

H bonds between NH and CO groups (further apart than alpha helix) to form parallel and anti-parallel strands.

What is the tertiary structure of a protein?

folding of a polypeptide chain due to interactions between side chains of amino acids that lie in different regions of the primary sequence

What determines the tertiary structure of a protein?

Non-covalent interactions between amino acid side chains

What are some qualities of a tertiary structure?

Tightly packed, thermodynamically stable, 3D

What are disulphide bridges?

Strong covalent bonds which form between cysteine residues and sulphur

What strengthens the tertiary structure of a protein?

Oxidation leads to cross links between parts of primary sequence of protein.

What is a protein domain?

any segment of a polypeptide chain that can fold independently into a compact, stable structure. Domains are separated by flexible regions that are less folded.

What do protein domains do?

Carry out specific parts of a proteins function

What is the quarternary structure of a protein?

when 2 or more polypeptide chains (subunits) are linked together. Dimer (2), trimer (3), tetramer (4)

How are proteins moved to the correct location after synthesis?

Proteins contain short signal/localisation sequence showing where they need to go

What are some post-translational modifications of proteins?

- Removal of sequence sections (signal peptides)
- Addition of small molecules (methylation, glycosylation, ubiquitination (marks out protein for degradation).

What is protein phosphorylation?

Reversible addition of phosphate group to a protein by a kinase (enzyme)

What does phosphorylation do?

Regulates enzyme function, changes properties of amino acids in/out of active sites and alters substrate binding

What did Gregor Mendel do?

Discovered laws of inheritance using pea plants
- Segregation
- Independent assortment
- Dominant and recessive alleles

How does DNA act as genetic material?

Passes on information to a new generation to influence an organism's characteristics

What did Walker Sutton and Theodor Boveri do in 1902?

- Studied early development of cells
- Sutton observed grasshoppers
- Boveri observed Ascaris worms
- Species studied as chromosomes were big and few in number
- Observed chromosomes grouped in pairs and subsequent separation lead to reduction in chromosome number in gametes
- Observations were consistent with Mendel's laws
- Suggested different combos of chromosomes can cause variation

What is the theory of inheritance?

genes are carried from parents to their offspring on chromosomes

What did Frederick Griffith do in 1928?

- Observed two strains of streptococcus pneumoniae, S strain (pathogenic), R strain (non-pathogenic)
- Wanted to know if strains were fixed
- Killed S strain with heat to obtain extracted
- Injected both strains into mice
- Observed whether bacteria in infected mice had a polysaccharide coat

What did Frederick Griffith discover?

- Inoculation with dead S bacteria and live R bacteria established infection
- Bacteria taken from the mouse had a polysaccharide coat
- Showed R bacteria had undergone transformation due to exchange of genetic material from S bacteria
- 'Tranformation principle'

What did Oswald Avery, Colin Macleod and Maclyn McCarthy do in 1944?

- Wanted to know what bacterial genetic material was made from
- Destroyed each component of S bacteria extract using enzymes
- Combined S bacteria with destroyed components with live R bacteria
- Found that DNA for polysaccharide coat is required for bacteria to be virulent

What did Alfred Hershey and Martha Chase do in 1952?

- Wanted to know which component of a bacteriophage was injected into bacteria
- Used T2 bacteria and E coli host
- Used unstable isotopes 32P and 35S
- bacteriophage grown in media containing 32P made phage containing radioactively labelled DNA
- Bacteriophage grown in media containing 35S made phage containing radioactively labelled protein
- mixture blended and centrifuged to separate phage (supernatant) from bacteria (pellet)
- Both fractions tested for radioactivity
- radioactively labelled DNA found in bacteria
Radioactively labelled protein found in phage
- Showed DNA was being passed on

What did Watson and Crick do?

used known information to determine the structure of DNA

What are the components of a nucleotide?

pentose sugar, phosphate group, nitrogenous base

Which bases are purines?

Adenine (A) and Guanine (G)

Which bases are pyrimidines?

Cytosine (C) and Thymine (T)

What bond is formed when two nucleotides join together?

Phosphodiester

How does a phosphodiester bond form?

Sugar of 1 nucleotide joins with phosphate group of another in a condensation reaction

What did Erwin Chargaff do?

-Used paper chromatography to work out ratios of components in DNA bases
- discovered the base pair rule:
A\=T
G\=C

What did Maurice Wilkins and Rosalind Franklin do?

they took x-ray crystallography photos of DNA
-they also said that DNA resembles tightly coiled helix

How many hydrogen bonds are between A and T

2 hydrogen bonds

How many hydrogen bonds are between C and G

3 hydrogen bonds

Describe the structure of DNA.

2 nucleotide strands running in opposite directions (antiparallel) coiled to form right-handed helices.
- DNA has major and minor groove

How many base pairs is one full turn of DNA

10.5 base pairs (3.4 nm)

What are chromosomes?

Chromosomes are long, thin strings of genetic material made of DNA and proteins.

What are histones?

proteins that DNA wraps around

How does the prokaryotic genome differ to the eukaryotic genome?

- Prokaryotes have 1 circular chromosome, eukaryotes have many linear chromosomes in a nucleus
- Prokaryotic genome is few million base pairs, eukaryotic genomes vary in size depending on the organism
- Prokaryotes contain plasmids which carry advantageous genes and are passed on via conjugation

What are centromeres?

the part of a chromosome that links sister chromatids and allows equal segregation during mitosis and meiosis

What is a telomere?

the ends of linear chromosomes, can be re-lengthened when DNA lost

What are DNA binding proteins?

- Proteins that bind to DNA sequences.
- Regulate gene expression.
- Cut DNA (nucleases)
- Activator and repressor proteins

What did Meselson and Stahl do?

Showed the DNA replicates through semiconservative replication

What is meant by semi-conservative replication?

When DNA replicates, two new molecules will have 1 strand of new, and one from original strand

What does DNA polymerase do?

Joins nucleotides to new strand in 5'-3' direction, uses template strand to form hydrogen bonds, add 10s-100s nucleotides per second

What does primase do?

synthesizes RNA primer which DNA polymerase uses as a template

What does ligase do?

joins Okazaki fragments together

What is a replication fork?

Where DNA strands separate

What is the leading strand in DNA replication?

the strand of DNA read by DNA polymerase pointing towards replication fork in 5'-3' direction

What is the lagging strand in DNA replication?

the strand of DNA read in fragments, points away from replication fork, must be primed multiple times

What does helicase do in DNA replication?

unwinds DNA by breaking hydrogen bonds

What does tropoisomerase do in DNA replication?

Relieves pressure and prevents overwinding around replication bubble by making and resealing breaks in DNA

What does the single strand binding protein do in DNA replication?

Binds to new strand to prevents original strand reannealing

What causes erosion of genetic material during replication?

- Primer removal at chromsome end (generates 3' overhang)
- Small piece of chromosome lost from lagging strand

How is erosion during replication fixed?

Telomeres

What does telomerase do?

It catalyses telomeres so they become longer and aren't affected too much by telomere erosion.

What is RNA?

A single stranded linear polymer of nucleotides containing ribose sugar

What is a nucleoside?

Ribose sugar and base

How many phosphates are lost when a triphosphate group is added to a ribose sugar to form a phosphodiester bond?

two

stem-loop structure

A sequence of RNA containing internal GC base pairing such that a hairpin loop forms during its transcription, which serves as a mechanism to terminate continued transcription.

stem loops

secondary structure of RNA, caused by sequences that are reverse-complements of each other. Helical structures of stem loops have a major and minor group.

What is canonical base pairing?

AU, GC

What is non-canonical base pairing?

GU 'wobble' base pair

What is an A-minor motif?

Most common tertiary interaction where 2 conservative A residues interact with adjacent base pairs in minor groove through sugar edge interactions.

What is RNA transcription?

Process by which RNA is made from double stranded DNA template

What does RNA transcription require?

- RNA polymerases (RNAPs)
- Coding strand
- Template strand

How does RNA transcription occur?

- RNA polymerase moves along coding strand in 5'-3' direction
- Nucleotide triphosphates (NTPs) are selected by base-pairing with template strand and added to 3' end of extending RNA strand

What does RNAP active site contain?

Short RNA/DNA heteroduplex

What is the RNA/DNA heteroduplex?

a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms.

How does RNA transcription end?

RNA polymerase directed to promoter regions of genes and continues until it reaches a terminator region (stop codon) and is released (heteroduplex becomes destabilised)

How can adjacent genes be transcribed?

in tandem, convergently or divergently

What is the E. coli RNAP core enzyme?

a protein complex containing 5 subunits ( 2 alpha, beta, beta prime and omega) that is capable of synthesising RNA without a DNA template

What do each of the subunits in the E. coli RNAP core enzyme do?

- Two alpha subunits bind to transcription factors
- Beta and beta prime subunits have catalytic properties
- Omega subunit involved in assembly and stability

What is a sigma factor?

a protein that associates with RNA polymerase that facilitates its binding to specific promoters

What happens when RNA polymerase binds to a sigma factor?

- RNA polymerase adopts an open and active conformation
- DNA active site is melted to form transcription bubble
- Short RNA primer is formed
- Sigma factor is released and RNAP moves away from promoter (promoter clearance) and becomes fully engaged in RNA synthesis
- RNAP can be re-used

What are the 3 eukaryotic RNAPs?

- RNAP I (transcribes rRNA)
- RNAP II (transcribes mRNA and non-coding RNAs)
- RNAP III transcribes tRNA and 5s RNA

Eukaryotic RNAPs

- Have common and unique subunits
- Conserved core structure homologous to bacterial enzyme

What do general transcription factors (GTFs) do?

Assemble RNAP II at eukaryotic gene promoters

What is the TATA box?

A DNA sequence in eukaryotic promotors crucial in forming the transcription initiation complex

What does the TATA box binding protein (TBP) in TFIID do?

Directly binds to DNA, causing DNA to bend, allowing recruitment of other factors