Since the inception of Wireless Local Area Networks (WLANs) in the year 1997, it has tremendously grown in the last few years. IEEE 802.11 is popularly known as WLAN. To provide the last mile wireless broadband connectivity to users, IEEE 802.11 is enriched with IEEE 802.11a, IEEE 802.11b and IEEE 802.11g. More recently, IEEE 802.11n, IEEE 802.11ac and IEEE 802.11ad are introduced with enhancements to the physical (PHY) layer and medium access control (MAC) sublayer to provide much higher data rates and thus these amendments are called High Throughput WLANs (HT-WLANs). In IEEE 802.11n, the data rate has increased up to 600 Mbps, whereas IEEE 802.11ac/ad is expected to support a maximum throughput of 1 to 7 Gbps over wireless media. For both standards, PHY is enhanced with multiple-input multiple-output (MIMO) antenna technologies, channel bonding, short guard intervals (SGI), enhanced modulation and coding schemes (MCS). At the same time, MAC layer overhead is reduced by introducing frame aggregation and block acknowledgement technologies. However, existing studies reveal that although PHY and MAC enhancements promise to improve physical data rate significantly, they yield negative impact over upper layer protocols -mainly for reliable end-to-end transport/application layer protocols. As a consequence, a large number of schools have focused researches on HT-WLANs to improve the coordination among PHY/MAC and upper layer protocols and thus, boost up the performance benefit. In this survey, we discuss the impact of enhancements of PHY/MAC layer in HT-WLANs over transport/application layer protocols. Several measures have been reported in the literature that boost up data rate of WLANs and use aforesaid enhancements effectively for performance benefit of end-to-end protocols. We also point out limitations of existing researches and list down different open challenges that can be explored for the development of next generation HT-WLAN technologies.