Biochem Week 2

What are chromosomes?

organised package of DNA found in the nucleus of the cell

What is a gene?

a sequence of nucleotides in DNA that encodes the synthesis of a protein

What is a nucleic acid?

polymers or nucleotides, there are 2 types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

What is a genome?

genetic material of an organism

What are genotypes?

complete set of genes of a cell, or organism

What is a phenotype?

features of a cell, or organism. it depends on expressed proteins and is regulated by the genotype, epigenetic modifications and environment

What are the three components of nucleotides?

-nitrogenous base -pentose (5-carbon) sugar -phosphate group

What are nitrogenous bases?

-information -purine: A or G -pyrimidine: T, C, U

What is Pentose?

-structure -deoxyribose (DNA) -ribose (RNA)

What is the phosphate group?

structure

How to distinguish between ribose and deoxyribose?

-carbon 2' on the pentose -presence or absence of a hydroxyl group (-OH) helps distinguish if it is a ribose (WITH -OH) or a deoxyribose (WITHOUT -OH)

What is a nucleoside?

base + sugar. a combination of a base and a sugar and are linked via a glycosidic bond

What is a nucleotide?

base + sugar + phosphate. formed when a phosphate group is bond to the hydroxyl group (-OH) of the 5' carbon in the sugar of the nucleoside

What are nucleic acids (polymers of nucleotides)?

connected via phosphate-group bridges (nucleotide chains are read from 5' to 3'

Why is DNA negative?

the phosphate group is negatively-charged

What other functions can nucleotides have?

-energy carriers -components of enzyme cofactors -chemical messengers

What are the structures in DNA?

-primary structure -secondary structure -tertiary structure -quaternary structure

What is primary structure?

the order of the nitrogenous bases (A, C, G, T) in the polynucleotide sequence specifies the genetic code

What is the secondary structure?

-DNA is a double helix that stores genetic information -DNA is formed by two complementary antiparallel strands (two strands with opposite directions) -the two strands are connected via hydrogen bonds between nitrogenous bases -G-C pairing is stronger than A-T

What is the Watson-Crick model?

-two complementary antiparallel strands held together by h-bonds -nitrogenous bases: information is protected inside the helix -pentose sugars: structure -phosphate groups: structure -diameter of DNA helix is about 20 A -major and minor groove in DNA are binding sites recognised by enzymes

What is the tertiary structure?

cellular DNA is extremely compact (the helix is supercoiled)

What is the quaternary structure?

-in eukaryotes, DNA is complexed with positively-charged proteins to form chromatin -DNA is wrapped around histones

What is DNA replication?

-each DNA strand serves as a template for the synthesis of a new strand -DNA helix is denatured to allow replication -each strand of DNA helix acts as a template for new complementary strand -dependent on complementary base pairing

What does Helicase do (DNA replication)?

unwinds the helix to form a replication fork

What does Primase do (DNA replication)?

synthesises short RNA primers, complementary to the template

What does DNA polymerase do (DNA replication)?

reads the existing strand and synthesises a new complementary strand, it links complementary nucleotides to form a new strand

What is the leading strand?

synthesised continuously from the template

What is the lagging strand?

synthesised with fragments (Okazaki fragments)

What does the DNA ligase do?

joins Ozaki fragments and seals the gaps in the newly synthesised short strands

How to obtain mRNA?

-mRNA is obtained by transcription of complementary section of DNA catalysed by RNA polymerase -transcription occurs in the nucleus

What does mRNA do?

-carries the information specifying a particular protein -mRNA molecules vary in length -mRNA molecule is translated into a polypeptide

What makes RNA unstable?

-the hydroxyl group (-OH) -the phosphodiester bond in the sugar-phosphate backbone of RNA is cleaved more easily because the -OH group facilitates chemical hydrolysis -the single-strand structure of RNA is more easily cleaved by enzymes

How is the unstable nature of RNA important for its role?

it is rapidly degraded after its activity is finished, while DNA is safely protected and kept inside the nucleus

What is transcription?

the information encoded in a gene in DNA is copied into a precursor messenger RNA molecule in the nucleus. the pre-mRNA transcript contains non-coding RNA and coding RNA, and is processed into mature mRNA

What is translation?

mature mRNA has the coding regions and moves to the cytoplasm. the information encoded by mature mRNA is converted into an amino acid sequence to obtain a functional protein

What is initiation?

-RNA polymerase binds to a promoter -it denatures the DNA locally

What is elongation?

-polymerase unwinds the DNA and the 3' to 5' strand serves as template -the mRNA transcripts are synthesised with the direction 5' to 3' -it is a very fast process

What is termination?

-the end of the DNA sequence is identified by a terminator sequence -mRNA transcript is released -DNA strands re-associate

What is RNA splicing?

the introns are removed from the pre-mRNA, and the exons are spliced together to form a continuous sequence that encodes for a functional polypeptide

What is 5' end cap?

a residue of 7-methylguanosine is linked to the 5' end of mRNA, to protect it from enzymatic degradation

What is 3' end cap?

a poly-A-tail is added to the 3' end of mRNA. it protects mRNA from enzymatic degradation and helps with the transcription termination

What do ribosomes do?

-cellular particle made of ribosomal RNA and proteins -it serves as the site for protein synthesis in the cell -it contains two subunits, which joins together to synthesise proteins -located in the cytoplasm -binds to mRNA and decodes the genetic code

What is rRNA?

-structural component of ribosomes -assists the reading of the mRNA and the synthesis of new proteins

What is tRNA?

-folds into a t shape, with some double strand regions -it has a recognition site -binds to a specific codon -it carries the corresponding amino acid